diff --git a/README.md b/README.md index 4ac4fc21d..68c7b5128 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,23 @@ Developed for reproducible & reusable molecular QTL analyses for the NIH/NIA Alzheimer's Disease Sequencing Project (ADSP) Functional Genomics xQTL (FunGen-xQTL) Project. +## What the protocol covers + +| Stage | What it does | +|---|---| +| **Molecular phenotypes** | Quantify expression, splicing, methylation and polyadenylation from bulk RNA-seq, single-nuclei or array data | +| **Data preprocessing** | Genotype QC and formatting, phenotype imputation and formatting, covariate and hidden-factor estimation | +| **QTL association testing** | cis and trans scans with TensorQTL, quantile-regression QTL, hierarchical multiple testing | +| **Multivariate modelling** | MASH, to borrow information across tissues and cell types | +| **Fine-mapping and TWAS** | SuSiE, mvSuSiE, fSuSiE and SuSiE-RSS, from individual-level data or summary statistics, with TWAS weights | +| **GWAS integration** | Colocalization (SuSiE-enloc, ColocBoost), TWAS and cTWAS, INTACT | +| **Enrichment and validation** | Pathway analysis, GREGOR, stratified LD score regression | + +Not every project needs every stage. The +[xQTL Analysis Workflow Builder](https://statfungen.github.io/xqtl-protocol/xqtl_protocol_workflow_builder.html) +asks what you measured and what you want to find out, then shows the modules on +that route with the commands to run them. + ## Getting started | I want to... | Go to | diff --git a/code/SoS/xqtl_protocol_demo.ipynb b/code/SoS/xqtl_protocol_demo.ipynb index 126fc2015..c829cedb1 100644 --- a/code/SoS/xqtl_protocol_demo.ipynb +++ b/code/SoS/xqtl_protocol_demo.ipynb @@ -232,7 +232,42 @@ "\n", "The demo on this page runs on a desktop workstation. Production analyses typically run on an HPC cluster, and SoS supports this natively via [SoS Remote Tasks](https://vatlab.github.io/sos-docs/doc/user_guide/task_statement.html) on [configured host computers](https://vatlab.github.io/sos-docs/doc/user_guide/host_setup.html).\n", "\n", - "We provide a [toy example for running SoS pipelines on a typical HPC cluster environment](https://github.com/statfungen/xqtl-protocol/blob/main/code/misc/Job_Example.ipynb) — first-time users are encouraged to work through it before launching real jobs. It covers the host and task configuration you'll reuse for every subsequent pipeline, and it's schedule-agnostic (SLURM, LSF, SGE, PBS/Torque all work).\n" + "We provide a [toy example for running SoS pipelines on a typical HPC cluster environment](https://github.com/statfungen/xqtl-protocol/blob/main/code/misc/Job_Example.ipynb) — first-time users are encouraged to work through it before launching real jobs. It covers the host and task configuration you'll reuse for every subsequent pipeline, and it's schedule-agnostic (SLURM, LSF, SGE, PBS/Torque all work).\n", + "\n", + "---\n", + "\n", + "## Using your own data\n", + "\n", + "The examples above run against files committed in `tests/fixtures/`. To run the same\n", + "pipeline on your own study, replace those paths with your own -- the parameters do\n", + "not change.\n", + "\n", + "Most modules expect some combination of:\n", + "\n", + "| Parameter | What it wants |\n", + "|---|---|\n", + "| `--genoFile` | Genotypes: PLINK `.bed/.bim/.fam`, or a list of per-chromosome files |\n", + "| `--phenoFile` | Molecular phenotype matrix: bgzipped BED, `#chr start end ID` then one column per sample |\n", + "| `--covFile` | Covariates, gzipped |\n", + "| `--region-list` | Regions to analyse, or a region list produced by an earlier step |\n", + "| `--cwd` | Where outputs are written |\n", + "\n", + "Sample identifiers must match across the genotype, phenotype and covariate files.\n", + "Most \"no overlapping samples\" errors come from a mismatch here rather than from a\n", + "problem with the data itself.\n", + "\n", + "To see the parameters a module accepts:\n", + "\n", + "```bash\n", + "sos run pipeline/.ipynb -h\n", + "```\n", + "\n", + "And for a set of arguments known to work, look at that module's test -- each one\n", + "carries a parameter set that CI runs:\n", + "\n", + "```bash\n", + "grep -rl 'run_sos' tests/notebooks --include='*.py'\n", + "```\n" ] } ], diff --git a/code/SoS/xqtl_protocol_workflow_builder.html b/code/SoS/xqtl_protocol_workflow_builder.html index 0e8766d09..92bf0e149 100644 --- a/code/SoS/xqtl_protocol_workflow_builder.html +++ b/code/SoS/xqtl_protocol_workflow_builder.html @@ -640,7 +640,7 @@

Your analysis route

return h; } let curBtn=null; -const BENCH={"twas_ctwas":{"seconds":311.3,"tests":1},"methylation_calling":{"seconds":250.9,"tests":2},"snRNAseq_preprocessing":{"seconds":221.1,"tests":3},"reference_data_preparation":{"seconds":195.6,"tests":13},"gsea":{"seconds":157.2,"tests":1},"mnm_postprocessing":{"seconds":152.9,"tests":7},"TensorQTL":{"seconds":147.6,"tests":3},"sldsc_enrichment":{"seconds":146.4,"tests":6},"mnm_regression":{"seconds":142.6,"tests":1},"rss_ld_sketch":{"seconds":113.2,"tests":6},"covariate_hidden_factor":{"seconds":113.2,"tests":7},"gene_annotation":{"seconds":99.1,"tests":5},"phenotype_imputation":{"seconds":95.9,"tests":10},"mash_fit":{"seconds":93.0,"tests":1},"phenotype_formatting":{"seconds":72.6,"tests":6},"rss_analysis":{"seconds":71.2,"tests":1},"PCA":{"seconds":67.8,"tests":5},"SuSiE_enloc":{"seconds":67.1,"tests":1},"colocboost":{"seconds":60.1,"tests":1},"mixture_prior":{"seconds":54.2,"tests":1},"qtl_association_postprocessing":{"seconds":28.6,"tests":1},"mash_preprocessing":{"seconds":24.9,"tests":1},"bulk_expression_QC":{"seconds":24.1,"tests":4},"apa_impute":{"seconds":23.5,"tests":1},"mash_posterior":{"seconds":22.7,"tests":1},"GWAS_QC":{"seconds":19.8,"tests":8},"intact":{"seconds":19.8,"tests":1},"eoo_enrichment":{"seconds":19.1,"tests":1},"gregor":{"seconds":18.7,"tests":2},"ems_training":{"seconds":14.8,"tests":3},"VCF_QC":{"seconds":12.4,"tests":5},"generalized_TADB":{"seconds":10.2,"tests":1},"covariate_formatting":{"seconds":9.9,"tests":2},"ld_prune_reference":{"seconds":7.4,"tests":2},"genotype_formatting":"23s on toy data (8 workflows)","splicing_normalization":"32s on toy data (4 workflows)","splicing_calling":"50s on toy data (5 workflows)","apa_calling":"22s on toy data (6 workflows)","RNA_calling":"1m 20s on toy data (16 workflows)","bulk_expression_normalization":"12s on toy data","pseudobulk_preprocessing":"30s on toy data (4 workflows)"},FIXTURES={"methylation_calling":{"dir":"tests/fixtures/methylation_calling","dirs":["tests/fixtures/methylation_calling","tests/fixtures/methylation_calling/expected"],"inputs":["tests/fixtures/methylation_calling/protocol_example.methylation.sample_sheet_int.csv"],"outputs":["tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sesame.beta.bed.gz","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sesame.M.bed.gz","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sesame.gene_id.annot.tsv","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sample_qcs.sesame.tsv"],"files":["tests/fixtures/methylation_calling/protocol_example.methylation.sample_sheet_int.csv","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sesame.beta.bed.gz","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sesame.M.bed.gz","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sesame.gene_id.annot.tsv","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sample_qcs.sesame.tsv"]},"GWAS_QC":{"dir":"tests/fixtures/gwas_qc","dirs":["tests/fixtures/gwas_qc","tests/fixtures/gwas_qc/expected"],"inputs":["tests/fixtures/gwas_qc/protocol_example.pheno.bed","tests/fixtures/gwas_qc/protocol_example.kin0"],"outputs":["tests/fixtures/gwas_qc/expected/king.kin0","tests/fixtures/gwas_qc/expected/king_2.related_id","tests/fixtures/gwas_qc/expected/king_split.unrelated.fam","tests/fixtures/gwas_qc/expected/king_split.related.fam","tests/fixtures/gwas_qc/expected/qc_no_prune.bim","tests/fixtures/gwas_qc/expected/qc_ld_prune.prune.in","tests/fixtures/gwas_qc/expected/qc_ld_prune.bim","tests/fixtures/gwas_qc/expected/sample_overlap.txt","tests/fixtures/gwas_qc/expected/king_workflow.unrelated.fam"],"files":["tests/fixtures/gwas_qc/protocol_example.pheno.bed","tests/fixtures/gwas_qc/protocol_example.kin0","tests/fixtures/gwas_qc/expected/king.kin0","tests/fixtures/gwas_qc/expected/king_2.related_id","tests/fixtures/gwas_qc/expected/king_split.unrelated.fam","tests/fixtures/gwas_qc/expected/king_split.related.fam","tests/fixtures/gwas_qc/expected/qc_no_prune.bim","tests/fixtures/gwas_qc/expected/qc_ld_prune.prune.in","tests/fixtures/gwas_qc/expected/qc_ld_prune.bim","tests/fixtures/gwas_qc/expected/sample_overlap.txt","tests/fixtures/gwas_qc/expected/king_workflow.unrelated.fam"]},"PCA":{"dir":"tests/fixtures/pca","dirs":["tests/fixtures/pca","tests/fixtures/pca/expected"],"inputs":["tests/fixtures/pca/protocol_example.pca_pheno.txt","tests/fixtures/pca/protocol_example.unrelated.prune.bed"],"outputs":["tests/fixtures/pca/expected/project_samples.rds","tests/fixtures/pca/expected/detect_outliers.maha.rds","tests/fixtures/pca/expected/detect_outliers.outliers.txt","tests/fixtures/pca/expected/pca_plink.eigenvec","tests/fixtures/pca/expected/flashpca.eigenvalues.tsv"],"files":["tests/fixtures/pca/protocol_example.pca_pheno.txt","tests/fixtures/pca/protocol_example.unrelated.prune.bed","tests/fixtures/pca/expected/project_samples.rds","tests/fixtures/pca/expected/detect_outliers.maha.rds","tests/fixtures/pca/expected/detect_outliers.outliers.txt","tests/fixtures/pca/expected/pca_plink.eigenvec","tests/fixtures/pca/expected/flashpca.eigenvalues.tsv"]},"RNA_calling":{"dir":"tests/fixtures/rna_calling","dirs":["tests/fixtures/rna_calling"],"inputs":["tests/fixtures/rna_calling/protocol_example.rnaseq.fastq.list.txt","tests/fixtures/rna_calling/SAMPLE_001.rnaseqc.metrics.tsv","tests/fixtures/rna_calling/SAMPLE_002.rnaseqc.metrics.tsv"],"outputs":[],"files":["tests/fixtures/rna_calling/protocol_example.rnaseq.fastq.list.txt","tests/fixtures/rna_calling/SAMPLE_001.rnaseqc.metrics.tsv","tests/fixtures/rna_calling/SAMPLE_002.rnaseqc.metrics.tsv"]},"SuSiE_enloc":{"dir":"tests/fixtures/susie_enloc","dirs":["tests/fixtures/susie_enloc","tests/fixtures/susie_enloc/expected"],"inputs":["tests/fixtures/susie_enloc/protocol_example.enloc.gwas_meta.tsv","tests/fixtures/susie_enloc/protocol_example.enloc.xqtl_meta.tsv"],"outputs":["tests/fixtures/susie_enloc/expected/coloc.rds","tests/fixtures/susie_enloc/expected/colocboost.rds","tests/fixtures/susie_enloc/expected/colocboost_manifest.tsv","tests/fixtures/susie_enloc/expected/enloc_manifest.enrichment.tsv","tests/fixtures/susie_enloc/expected/enloc_manifest.coloc.tsv"],"files":["tests/fixtures/susie_enloc/protocol_example.enloc.gwas_meta.tsv","tests/fixtures/susie_enloc/protocol_example.enloc.xqtl_meta.tsv","tests/fixtures/susie_enloc/expected/coloc.rds","tests/fixtures/susie_enloc/expected/colocboost.rds","tests/fixtures/susie_enloc/expected/colocboost_manifest.tsv","tests/fixtures/susie_enloc/expected/enloc_manifest.enrichment.tsv","tests/fixtures/susie_enloc/expected/enloc_manifest.coloc.tsv"]},"VCF_QC":{"dir":"tests/fixtures/vcf_qc","dirs":["tests/fixtures/vcf_qc","tests/fixtures/vcf_qc/expected"],"inputs":["tests/fixtures/vcf_qc/numeric_chr22.vcf.gz","tests/fixtures/vcf_qc/genotype.chr22_48M.vcf.gz"],"outputs":["tests/fixtures/vcf_qc/expected/rename_chrs.variants.tsv","tests/fixtures/vcf_qc/expected/qc_normalize.variants.tsv","tests/fixtures/vcf_qc/expected/qc_2.variants.tsv","tests/fixtures/vcf_qc/expected/qc_3.novel.tstv","tests/fixtures/vcf_qc/expected/qc_3.known.tstv"],"files":["tests/fixtures/vcf_qc/numeric_chr22.vcf.gz","tests/fixtures/vcf_qc/genotype.chr22_48M.vcf.gz","tests/fixtures/vcf_qc/expected/rename_chrs.variants.tsv","tests/fixtures/vcf_qc/expected/qc_normalize.variants.tsv","tests/fixtures/vcf_qc/expected/qc_2.variants.tsv","tests/fixtures/vcf_qc/expected/qc_3.novel.tstv","tests/fixtures/vcf_qc/expected/qc_3.known.tstv"]},"apa_calling":{"dir":"tests/fixtures/apa_calling","dirs":["tests/fixtures/apa_calling"],"inputs":["tests/fixtures/apa_calling/depth.txt","tests/fixtures/apa_calling/chr22_3UTR.bed","tests/fixtures/apa_calling/chr22.hdr.gtf.gz"],"outputs":[],"files":["tests/fixtures/apa_calling/depth.txt","tests/fixtures/apa_calling/chr22_3UTR.bed","tests/fixtures/apa_calling/chr22.hdr.gtf.gz"]},"apa_impute":{"dir":"tests/fixtures/apa_impute","dirs":["tests/fixtures/apa_impute","tests/fixtures/apa_impute/apa_chr22","tests/fixtures/apa_impute/expected"],"inputs":["tests/fixtures/apa_impute/protocol_example.apa_matchtable.txt","tests/fixtures/apa_impute/apa_chr22/Dapars_result_result_temp.chr22.txt"],"outputs":["tests/fixtures/apa_impute/expected/expected.Dapars_result_impute_chr22.bed","tests/fixtures/apa_impute/expected/expected.Dapars_allchrom.bed","tests/fixtures/apa_impute/expected/expected.Dapars_result_impute_renamed_chr22.bed.gz","tests/fixtures/apa_impute/expected/expected.Dapars_allchrom_renamed.bed"],"files":["tests/fixtures/apa_impute/protocol_example.apa_matchtable.txt","tests/fixtures/apa_impute/apa_chr22/Dapars_result_result_temp.chr22.txt","tests/fixtures/apa_impute/expected/expected.Dapars_result_impute_chr22.bed","tests/fixtures/apa_impute/expected/expected.Dapars_allchrom.bed","tests/fixtures/apa_impute/expected/expected.Dapars_result_impute_renamed_chr22.bed.gz","tests/fixtures/apa_impute/expected/expected.Dapars_allchrom_renamed.bed"]},"bulk_expression_normalization":{"dir":"tests/fixtures/bulk_expression_normalization","dirs":["tests/fixtures/bulk_expression_normalization","tests/fixtures/bulk_expression_normalization/expected"],"inputs":["tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.geneCount.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.sample_participant_lookup.txt"],"outputs":["tests/fixtures/bulk_expression_normalization/expected/expected.qc_1.low_expression_filtered.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_2.outlier_removed.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_3.outlier_removed.geneCount.gct.gz"],"files":["tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.geneCount.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.sample_participant_lookup.txt","tests/fixtures/bulk_expression_normalization/expected/expected.qc_1.low_expression_filtered.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_2.outlier_removed.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_3.outlier_removed.geneCount.gct.gz"]},"colocboost":{"dir":"tests/fixtures/colocboost","dirs":["tests/fixtures/colocboost/expected"],"inputs":[],"outputs":["tests/fixtures/colocboost/expected/test_coloc.ENSG00000283047.colocboost.rds"],"files":["tests/fixtures/colocboost/expected/test_coloc.ENSG00000283047.colocboost.rds"]},"covariate_formatting":{"dir":"tests/fixtures/covariate_formatting","dirs":["tests/fixtures/covariate_formatting","tests/fixtures/covariate_formatting/expected"],"inputs":["tests/fixtures/covariate_formatting/covariates.base.tsv"],"outputs":["tests/fixtures/covariate_formatting/expected/merged.gz"],"files":["tests/fixtures/covariate_formatting/covariates.base.tsv","tests/fixtures/covariate_formatting/expected/merged.gz"]},"covariate_hidden_factor":{"dir":"tests/fixtures/covariate_hidden_factor","dirs":["tests/fixtures/covariate_hidden_factor","tests/fixtures/covariate_hidden_factor/expected"],"inputs":["tests/fixtures/covariate_hidden_factor/covariates.tsv"],"outputs":["tests/fixtures/covariate_hidden_factor/expected/residual.bed.gz","tests/fixtures/covariate_hidden_factor/expected/Marchenko_PC.gz","tests/fixtures/covariate_hidden_factor/expected/Buja_Eyuboglu_PC.gz","tests/fixtures/covariate_hidden_factor/expected/PEER.factors.tsv","tests/fixtures/covariate_hidden_factor/expected/PEER.weights.tsv","tests/fixtures/covariate_hidden_factor/expected/PEER.variance.tsv","tests/fixtures/covariate_hidden_factor/expected/PEER.gz"],"files":["tests/fixtures/covariate_hidden_factor/covariates.tsv","tests/fixtures/covariate_hidden_factor/expected/residual.bed.gz","tests/fixtures/covariate_hidden_factor/expected/Marchenko_PC.gz","tests/fixtures/covariate_hidden_factor/expected/Buja_Eyuboglu_PC.gz","tests/fixtures/covariate_hidden_factor/expected/PEER.factors.tsv","tests/fixtures/covariate_hidden_factor/expected/PEER.weights.tsv","tests/fixtures/covariate_hidden_factor/expected/PEER.variance.tsv","tests/fixtures/covariate_hidden_factor/expected/PEER.gz"]},"ems_prediction":{"dir":"tests/fixtures/ems_training","dirs":["tests/fixtures/ems_training","tests/fixtures/ems_training/expected"],"inputs":["tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr1.tsv","tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr2.tsv","tests/fixtures/ems_training/model_config.yaml"],"outputs":["tests/fixtures/ems_training/expected/features_importance_model5_chr_chr2_NPR_1.csv","tests/fixtures/ems_training/expected/model_5_summary_chr_chr2_NPR_1.json","tests/fixtures/ems_training/expected/predictions_weighted_model_chr2.tsv"],"files":["tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr1.tsv","tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr2.tsv","tests/fixtures/ems_training/model_config.yaml","tests/fixtures/ems_training/expected/features_importance_model5_chr_chr2_NPR_1.csv","tests/fixtures/ems_training/expected/model_5_summary_chr_chr2_NPR_1.json","tests/fixtures/ems_training/expected/predictions_weighted_model_chr2.tsv"]},"ems_training":{"dir":"tests/fixtures/ems_training","dirs":["tests/fixtures/ems_training","tests/fixtures/ems_training/expected"],"inputs":["tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr1.tsv","tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr2.tsv","tests/fixtures/ems_training/model_config.yaml"],"outputs":["tests/fixtures/ems_training/expected/features_importance_model5_chr_chr2_NPR_1.csv","tests/fixtures/ems_training/expected/model_5_summary_chr_chr2_NPR_1.json","tests/fixtures/ems_training/expected/predictions_weighted_model_chr2.tsv"],"files":["tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr1.tsv","tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr2.tsv","tests/fixtures/ems_training/model_config.yaml","tests/fixtures/ems_training/expected/features_importance_model5_chr_chr2_NPR_1.csv","tests/fixtures/ems_training/expected/model_5_summary_chr_chr2_NPR_1.json","tests/fixtures/ems_training/expected/predictions_weighted_model_chr2.tsv"]},"eoo_enrichment":{"dir":"tests/fixtures/eoo_enrichment","dirs":["tests/fixtures/eoo_enrichment","tests/fixtures/eoo_enrichment/expected"],"inputs":["tests/fixtures/eoo_enrichment/protocol_example.eoo_baseline_annotation.tsv.gz","tests/fixtures/eoo_enrichment/protocol_example.eoo_significant_variants.tsv.gz"],"outputs":["tests/fixtures/eoo_enrichment/expected/enrichment_results.rds","tests/fixtures/eoo_enrichment/expected/enrichment_results_summary.tsv.gz"],"files":["tests/fixtures/eoo_enrichment/protocol_example.eoo_baseline_annotation.tsv.gz","tests/fixtures/eoo_enrichment/protocol_example.eoo_significant_variants.tsv.gz","tests/fixtures/eoo_enrichment/expected/enrichment_results.rds","tests/fixtures/eoo_enrichment/expected/enrichment_results_summary.tsv.gz"]},"gene_annotation":{"dir":"tests/fixtures/gene_annotation","dirs":["tests/fixtures/gene_annotation","tests/fixtures/gene_annotation/expected"],"inputs":["tests/fixtures/gene_annotation/protocol_example.atac.tsv","tests/fixtures/gene_annotation/protocol_example.rnaseq.bed.gz"],"outputs":["tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.gene_list.tsv","tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.region_list.txt","tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.gene_list.tsv","tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.region_list.txt","tests/fixtures/gene_annotation/expected/protocol_example.atac.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.atac.region_list.txt","tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.intron_count.tsv.leafcutter.clusters_to_genes.txt","tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.phenotype.bed.formated.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.phenotype.bed.phenotype_group.txt","tests/fixtures/gene_annotation/expected/protocol_example.psichomics.phenotype.formated.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.psichomics.phenotype.phenotype_group.txt"],"files":["tests/fixtures/gene_annotation/protocol_example.atac.tsv","tests/fixtures/gene_annotation/protocol_example.rnaseq.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.gene_list.tsv","tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.region_list.txt","tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.gene_list.tsv","tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.region_list.txt","tests/fixtures/gene_annotation/expected/protocol_example.atac.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.atac.region_list.txt","tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.intron_count.tsv.leafcutter.clusters_to_genes.txt","tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.phenotype.bed.formated.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.phenotype.bed.phenotype_group.txt","tests/fixtures/gene_annotation/expected/protocol_example.psichomics.phenotype.formated.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.psichomics.phenotype.phenotype_group.txt"]},"generalized_TADB":{"dir":"tests/fixtures/generalized_TADB","dirs":["tests/fixtures/generalized_TADB","tests/fixtures/generalized_TADB/expected"],"inputs":["tests/fixtures/generalized_TADB/protocol_example.brain_TADs.txt","tests/fixtures/generalized_TADB/protocol_example.gene_start_end.tsv"],"outputs":["tests/fixtures/generalized_TADB/expected/generalized_TAD.tsv","tests/fixtures/generalized_TADB/expected/generalized_TADB.tsv","tests/fixtures/generalized_TADB/expected/TADB_enhanced_cis.bed","tests/fixtures/generalized_TADB/expected/extended_TADB.bed"],"files":["tests/fixtures/generalized_TADB/protocol_example.brain_TADs.txt","tests/fixtures/generalized_TADB/protocol_example.gene_start_end.tsv","tests/fixtures/generalized_TADB/expected/generalized_TAD.tsv","tests/fixtures/generalized_TADB/expected/generalized_TADB.tsv","tests/fixtures/generalized_TADB/expected/TADB_enhanced_cis.bed","tests/fixtures/generalized_TADB/expected/extended_TADB.bed"]},"genotype_formatting":{"dir":"tests/fixtures/genotype_formatting","dirs":["tests/fixtures/genotype_formatting/geno","tests/fixtures/genotype_formatting/expected"],"inputs":["tests/fixtures/genotype_formatting/geno/chr21.bed","tests/fixtures/genotype_formatting/geno/chr21.bim"],"outputs":["tests/fixtures/genotype_formatting/expected/ld_by_region.float16.rds","tests/fixtures/genotype_formatting/expected/plink_to_vcf.variants.tsv","tests/fixtures/genotype_formatting/expected/vcf_to_plink.bim","tests/fixtures/genotype_formatting/expected/genotype_by_region.bim","tests/fixtures/genotype_formatting/expected/genotype_by_chrom.bim"],"files":["tests/fixtures/genotype_formatting/geno/chr21.bed","tests/fixtures/genotype_formatting/geno/chr21.bim","tests/fixtures/genotype_formatting/expected/ld_by_region.float16.rds","tests/fixtures/genotype_formatting/expected/plink_to_vcf.variants.tsv","tests/fixtures/genotype_formatting/expected/vcf_to_plink.bim","tests/fixtures/genotype_formatting/expected/genotype_by_region.bim","tests/fixtures/genotype_formatting/expected/genotype_by_chrom.bim"]},"gregor":{"dir":"tests/fixtures/gregor","dirs":["tests/fixtures/gregor","tests/fixtures/gregor/expected"],"inputs":["tests/fixtures/gregor/index.snps.txt","tests/fixtures/gregor/test_peaks.bed","tests/fixtures/gregor/example_enrichment_results.txt"],"outputs":["tests/fixtures/gregor/expected/enrichment_results.txt"],"files":["tests/fixtures/gregor/index.snps.txt","tests/fixtures/gregor/test_peaks.bed","tests/fixtures/gregor/example_enrichment_results.txt","tests/fixtures/gregor/expected/enrichment_results.txt"]},"gsea":{"dir":"tests/fixtures/gsea","dirs":["tests/fixtures/gsea","tests/fixtures/gsea/expected"],"inputs":["tests/fixtures/gsea/protocol_example.pathway_genes.tsv"],"outputs":["tests/fixtures/gsea/expected/pathway_go_results.rds"],"files":["tests/fixtures/gsea/protocol_example.pathway_genes.tsv","tests/fixtures/gsea/expected/pathway_go_results.rds"]},"intact":{"dir":"tests/fixtures/intact","dirs":["tests/fixtures/intact","tests/fixtures/intact/expected"],"inputs":["tests/fixtures/intact/README.md","tests/fixtures/intact/protocol_example.ptwas.output"],"outputs":["tests/fixtures/intact/expected/intact.rds"],"files":["tests/fixtures/intact/README.md","tests/fixtures/intact/protocol_example.ptwas.output","tests/fixtures/intact/expected/intact.rds"]},"ld_prune_reference":{"dir":"tests/fixtures/ld_prune_reference","dirs":["tests/fixtures/ld_prune_reference/genotype"],"inputs":["tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.bed","tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.bim","tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.fam"],"outputs":[],"files":["tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.bed","tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.bim","tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.fam"]},"mash_fit":{"dir":"tests/fixtures/mash","dirs":["tests/fixtures/mash","tests/fixtures/mash/expected"],"inputs":["tests/fixtures/mash/mashr_input.rds","tests/fixtures/mash/region_strong.rds","tests/fixtures/mash/Ast_De_Jager_eQTL.tsv"],"outputs":["tests/fixtures/mash/expected/mash_model.EE.rds"],"files":["tests/fixtures/mash/mashr_input.rds","tests/fixtures/mash/region_strong.rds","tests/fixtures/mash/Ast_De_Jager_eQTL.tsv","tests/fixtures/mash/expected/mash_model.EE.rds"]},"mash_posterior":{"dir":"tests/fixtures/mash_posterior","dirs":["tests/fixtures/mash_posterior"],"inputs":["tests/fixtures/mash_posterior/orig.rds","tests/fixtures/mash_posterior/posterior.rds","tests/fixtures/mash_posterior/fine_mapping.rds"],"outputs":[],"files":["tests/fixtures/mash_posterior/orig.rds","tests/fixtures/mash_posterior/posterior.rds","tests/fixtures/mash_posterior/fine_mapping.rds"]},"mash_preprocessing":{"dir":"tests/fixtures/mash","dirs":["tests/fixtures/mash","tests/fixtures/mash/expected"],"inputs":["tests/fixtures/mash/mashr_input.rds","tests/fixtures/mash/region_strong.rds","tests/fixtures/mash/Ast_De_Jager_eQTL.tsv"],"outputs":["tests/fixtures/mash/expected/mash_sumstats.region1.rds","tests/fixtures/mash/expected/mash_input.qss.rds","tests/fixtures/mash/expected/mash_input.fmr.rds","tests/fixtures/mash/expected/mash_input.indep.rds"],"files":["tests/fixtures/mash/mashr_input.rds","tests/fixtures/mash/region_strong.rds","tests/fixtures/mash/Ast_De_Jager_eQTL.tsv","tests/fixtures/mash/expected/mash_sumstats.region1.rds","tests/fixtures/mash/expected/mash_input.qss.rds","tests/fixtures/mash/expected/mash_input.fmr.rds","tests/fixtures/mash/expected/mash_input.indep.rds"]},"mixture_prior":{"dir":"tests/fixtures/mash","dirs":["tests/fixtures/mash","tests/fixtures/mash/expected"],"inputs":["tests/fixtures/mash/mashr_input.rds","tests/fixtures/mash/region_strong.rds","tests/fixtures/mash/Ast_De_Jager_eQTL.tsv"],"outputs":["tests/fixtures/mash/expected/mixture_prior.EE.prior.rds","tests/fixtures/mash/expected/vhat.identity.EE.rds","tests/fixtures/mash/expected/vhat.simple.EE.rds","tests/fixtures/mash/expected/vhat.corshrink.EE.rds","tests/fixtures/mash/expected/vhat.simple_specific.EE.rds","tests/fixtures/mash/expected/prior.cov_ed.EE.rds","tests/fixtures/mash/expected/cov.canonical.EE.rds","tests/fixtures/mash/expected/cov.pca.EE.rds","tests/fixtures/mash/expected/cov.flash.EE.rds","tests/fixtures/mash/expected/cov.flash_nonneg.EE.rds"],"files":["tests/fixtures/mash/mashr_input.rds","tests/fixtures/mash/region_strong.rds","tests/fixtures/mash/Ast_De_Jager_eQTL.tsv","tests/fixtures/mash/expected/mixture_prior.EE.prior.rds","tests/fixtures/mash/expected/vhat.identity.EE.rds","tests/fixtures/mash/expected/vhat.simple.EE.rds","tests/fixtures/mash/expected/vhat.corshrink.EE.rds","tests/fixtures/mash/expected/vhat.simple_specific.EE.rds","tests/fixtures/mash/expected/prior.cov_ed.EE.rds","tests/fixtures/mash/expected/cov.canonical.EE.rds","tests/fixtures/mash/expected/cov.pca.EE.rds","tests/fixtures/mash/expected/cov.flash.EE.rds","tests/fixtures/mash/expected/cov.flash_nonneg.EE.rds"]},"phenotype_formatting":{"dir":"tests/fixtures/phenotype_formatting","dirs":["tests/fixtures/phenotype_formatting","tests/fixtures/phenotype_formatting/expected","tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region"],"inputs":["tests/fixtures/phenotype_formatting/regions.txt","tests/fixtures/phenotype_formatting/tad_list.txt","tests/fixtures/phenotype_formatting/keep_samples.txt"],"outputs":["tests/fixtures/phenotype_formatting/expected/protocol_example.chr22.bed.gz","tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_chrom_files.txt","tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_chrom_files.region_list.txt","tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region/protocol_example.region1.bed.gz","tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region/protocol_example.region2.bed.gz","tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_region_files.txt","tests/fixtures/phenotype_formatting/expected/protocol_example.tpm.sample_matched.gct.gz","tests/fixtures/phenotype_formatting/expected/protocol_example.rnaseq.bed.bed.gz.tad_list.txt.2_pheno_per_region.region_list","tests/fixtures/phenotype_formatting/expected/protocol_example.chr22.gct"],"files":["tests/fixtures/phenotype_formatting/regions.txt","tests/fixtures/phenotype_formatting/tad_list.txt","tests/fixtures/phenotype_formatting/keep_samples.txt","tests/fixtures/phenotype_formatting/expected/protocol_example.chr22.bed.gz","tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_chrom_files.txt","tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_chrom_files.region_list.txt","tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region/protocol_example.region1.bed.gz","tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region/protocol_example.region2.bed.gz","tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_region_files.txt","tests/fixtures/phenotype_formatting/expected/protocol_example.tpm.sample_matched.gct.gz","tests/fixtures/phenotype_formatting/expected/protocol_example.rnaseq.bed.bed.gz.tad_list.txt.2_pheno_per_region.region_list","tests/fixtures/phenotype_formatting/expected/protocol_example.chr22.gct"]},"phenotype_imputation":{"dir":"tests/fixtures/phenotype_imputation","dirs":["tests/fixtures/phenotype_imputation","tests/fixtures/phenotype_imputation/expected"],"inputs":["tests/fixtures/phenotype_imputation/protocol_example.protein.missing.bed.gz"],"outputs":["tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.EBMF.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.knn.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.mean.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.lod.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.soft.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.filtered.imputed.bed.gz"],"files":["tests/fixtures/phenotype_imputation/protocol_example.protein.missing.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.EBMF.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.knn.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.mean.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.lod.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.soft.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.filtered.imputed.bed.gz"]},"pseudobulk_preprocessing":{"dir":"tests/fixtures/pseudobulk_preprocessing","dirs":["tests/fixtures/pseudobulk_preprocessing","tests/fixtures/pseudobulk_preprocessing/expected"],"inputs":["tests/fixtures/pseudobulk_preprocessing/protocol_example.snrnaseq.seurat_MIC.rds","tests/fixtures/pseudobulk_preprocessing/counts_MIC.csv.gz","tests/fixtures/pseudobulk_preprocessing/atac_MIC_residuals.txt"],"outputs":["tests/fixtures/pseudobulk_preprocessing/expected/expected_counts_MIC.remapped.csv.gz","tests/fixtures/pseudobulk_preprocessing/expected/expected_MIC_residuals_qn.txt"],"files":["tests/fixtures/pseudobulk_preprocessing/protocol_example.snrnaseq.seurat_MIC.rds","tests/fixtures/pseudobulk_preprocessing/counts_MIC.csv.gz","tests/fixtures/pseudobulk_preprocessing/atac_MIC_residuals.txt","tests/fixtures/pseudobulk_preprocessing/expected/expected_counts_MIC.remapped.csv.gz","tests/fixtures/pseudobulk_preprocessing/expected/expected_MIC_residuals_qn.txt"]},"qtl_association_postprocessing":{"dir":"tests/fixtures/qtl_association_postprocessing","dirs":["tests/fixtures/qtl_association_postprocessing","tests/fixtures/qtl_association_postprocessing/expected"],"inputs":["tests/fixtures/qtl_association_postprocessing/protocol_example.cis_qtl.pairs.tsv.gz","tests/fixtures/qtl_association_postprocessing/protocol_example.cis_qtl.regional.tsv.gz","tests/fixtures/qtl_association_postprocessing/protocol_example.maf_0.01_window_1000000_cis_n_variants_stats.tsv.gz"],"outputs":["tests/fixtures/qtl_association_postprocessing/expected/qap.rds","tests/fixtures/qtl_association_postprocessing/expected/qap.cis_regional.fdr.tsv.gz","tests/fixtures/qtl_association_postprocessing/expected/qap.summary.tsv"],"files":["tests/fixtures/qtl_association_postprocessing/protocol_example.cis_qtl.pairs.tsv.gz","tests/fixtures/qtl_association_postprocessing/protocol_example.cis_qtl.regional.tsv.gz","tests/fixtures/qtl_association_postprocessing/protocol_example.maf_0.01_window_1000000_cis_n_variants_stats.tsv.gz","tests/fixtures/qtl_association_postprocessing/expected/qap.rds","tests/fixtures/qtl_association_postprocessing/expected/qap.cis_regional.fdr.tsv.gz","tests/fixtures/qtl_association_postprocessing/expected/qap.summary.tsv"]},"reference_data_preparation":{"dir":"tests/fixtures/reference_data_preparation","dirs":["tests/fixtures/reference_data_preparation","tests/fixtures/reference_data_preparation/expected"],"inputs":["tests/fixtures/reference_data_preparation/hgnc_chr22.tsv.gz","tests/fixtures/reference_data_preparation/mini.gff3","tests/fixtures/reference_data_preparation/ERCC92.gtf"],"outputs":["tests/fixtures/reference_data_preparation/expected/hg_reference_1.filtered.fasta","tests/fixtures/reference_data_preparation/expected/hg_gtf_1.reformatted.gtf","tests/fixtures/reference_data_preparation/expected/faidx.test_contigs.fa.fai","tests/fixtures/reference_data_preparation/expected/mini.gtf","tests/fixtures/reference_data_preparation/expected/hg38.chr22_SE_strict.ioe","tests/fixtures/reference_data_preparation/expected/chr22.SUPPA_annotation.rds"],"files":["tests/fixtures/reference_data_preparation/hgnc_chr22.tsv.gz","tests/fixtures/reference_data_preparation/mini.gff3","tests/fixtures/reference_data_preparation/ERCC92.gtf","tests/fixtures/reference_data_preparation/expected/hg_reference_1.filtered.fasta","tests/fixtures/reference_data_preparation/expected/hg_gtf_1.reformatted.gtf","tests/fixtures/reference_data_preparation/expected/faidx.test_contigs.fa.fai","tests/fixtures/reference_data_preparation/expected/mini.gtf","tests/fixtures/reference_data_preparation/expected/hg38.chr22_SE_strict.ioe","tests/fixtures/reference_data_preparation/expected/chr22.SUPPA_annotation.rds"]},"rss_analysis":{"dir":"tests/fixtures/rss_analysis","dirs":["tests/fixtures/rss_analysis","tests/fixtures/rss_analysis/expected"],"inputs":["tests/fixtures/rss_analysis/protocol_example.rss_mwe.gwas_meta.tsv","tests/fixtures/rss_analysis/protocol_example.gwas_sumstats.chr22.tsv.gz","tests/fixtures/rss_analysis/protocol_example.gwas_column_mapping.yml"],"outputs":["tests/fixtures/rss_analysis/expected/gwas_sumstats.rds","tests/fixtures/rss_analysis/expected/gwas_finemap.rds"],"files":["tests/fixtures/rss_analysis/protocol_example.rss_mwe.gwas_meta.tsv","tests/fixtures/rss_analysis/protocol_example.gwas_sumstats.chr22.tsv.gz","tests/fixtures/rss_analysis/protocol_example.gwas_column_mapping.yml","tests/fixtures/rss_analysis/expected/gwas_sumstats.rds","tests/fixtures/rss_analysis/expected/gwas_finemap.rds"]},"rss_ld_sketch":{"dir":"tests/fixtures/rss_ld_sketch","dirs":["tests/fixtures/rss_ld_sketch"],"inputs":["tests/fixtures/rss_ld_sketch/protocol_example.ld_blocks.bed","tests/fixtures/rss_ld_sketch/protocol_example.genotype.chr22.vcf.gz","tests/fixtures/rss_ld_sketch/protocol_example.genotype.chr22.vcf.gz.tbi"],"outputs":[],"files":["tests/fixtures/rss_ld_sketch/protocol_example.ld_blocks.bed","tests/fixtures/rss_ld_sketch/protocol_example.genotype.chr22.vcf.gz","tests/fixtures/rss_ld_sketch/protocol_example.genotype.chr22.vcf.gz.tbi"]},"sldsc_enrichment":{"dir":"tests/fixtures/sldsc_enrichment","dirs":["tests/fixtures/sldsc_enrichment","tests/fixtures/sldsc_enrichment/expected"],"inputs":["tests/fixtures/sldsc_enrichment/target.tsv","tests/fixtures/sldsc_enrichment/reference.2.bed","tests/fixtures/sldsc_enrichment/reference.2.bim"],"outputs":["tests/fixtures/sldsc_enrichment/expected/sldsc_postprocess.rds","tests/fixtures/sldsc_enrichment/expected/sldsc_meta_subset.rds","tests/fixtures/sldsc_enrichment/expected/sldsc_meta_subset.notebook.rds"],"files":["tests/fixtures/sldsc_enrichment/target.tsv","tests/fixtures/sldsc_enrichment/reference.2.bed","tests/fixtures/sldsc_enrichment/reference.2.bim","tests/fixtures/sldsc_enrichment/expected/sldsc_postprocess.rds","tests/fixtures/sldsc_enrichment/expected/sldsc_meta_subset.rds","tests/fixtures/sldsc_enrichment/expected/sldsc_meta_subset.notebook.rds"]},"snRNAseq_preprocessing":{"dir":"tests/fixtures/snrnaseq_preprocessing","dirs":["tests/fixtures/snrnaseq_preprocessing"],"inputs":["tests/fixtures/snrnaseq_preprocessing/protocol_example.snrnaseq.seurat_ref_SE.rds","tests/fixtures/snrnaseq_preprocessing/protocol_example.snrnaseq.id_mapping.csv"],"outputs":[],"files":["tests/fixtures/snrnaseq_preprocessing/protocol_example.snrnaseq.seurat_ref_SE.rds","tests/fixtures/snrnaseq_preprocessing/protocol_example.snrnaseq.id_mapping.csv"]},"splicing_calling":{"dir":"tests/fixtures/splicing_calling","dirs":["tests/fixtures/splicing_calling/leafcutter","tests/fixtures/splicing_calling/psichomics"],"inputs":["tests/fixtures/splicing_calling/leafcutter/SAMPLE_001.junc.gz","tests/fixtures/splicing_calling/leafcutter/SAMPLE_002.junc.gz"],"outputs":["tests/fixtures/splicing_calling/psichomics/expected_junctions.txt"],"files":["tests/fixtures/splicing_calling/leafcutter/SAMPLE_001.junc.gz","tests/fixtures/splicing_calling/leafcutter/SAMPLE_002.junc.gz","tests/fixtures/splicing_calling/psichomics/expected_junctions.txt"]},"splicing_normalization":{"dir":"tests/fixtures/splicing_normalization","dirs":["tests/fixtures/splicing_normalization","tests/fixtures/splicing_normalization/expected"],"inputs":["tests/fixtures/splicing_normalization/raw_data.txt.gz","tests/fixtures/splicing_normalization/psi_raw_data.tsv.gz"],"outputs":["tests/fixtures/splicing_normalization/expected.phen_chr22.gz","tests/fixtures/splicing_normalization/expected/expected.prepare_phenotype.ave","tests/fixtures/splicing_normalization/expected/expected.prepare_phenotype.phenotype_file_list.txt"],"files":["tests/fixtures/splicing_normalization/raw_data.txt.gz","tests/fixtures/splicing_normalization/psi_raw_data.tsv.gz","tests/fixtures/splicing_normalization/expected.phen_chr22.gz","tests/fixtures/splicing_normalization/expected/expected.prepare_phenotype.ave","tests/fixtures/splicing_normalization/expected/expected.prepare_phenotype.phenotype_file_list.txt"]},"twas_ctwas":{"dir":"tests/fixtures/twas","dirs":["tests/fixtures/twas","tests/fixtures/twas/expected"],"inputs":["tests/fixtures/twas/protocol_example.twas.gwas_meta.tsv","tests/fixtures/twas/protocol_example.twas.xqtl_meta.tsv"],"outputs":["tests/fixtures/twas/expected/gwas_sumstats.chr22.rds","tests/fixtures/twas/expected/twas.chr22.rds"],"files":["tests/fixtures/twas/protocol_example.twas.gwas_meta.tsv","tests/fixtures/twas/protocol_example.twas.xqtl_meta.tsv","tests/fixtures/twas/expected/gwas_sumstats.chr22.rds","tests/fixtures/twas/expected/twas.chr22.rds"]},"TensorQTL":{"dir":"tests/fixtures","dirs":["tests/fixtures/qtl_mini","tests/fixtures/tensorqtl/expected"],"inputs":["tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bed","tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bim","tests/fixtures/qtl_mini/protocol_example.genotype.chr22.fam","tests/fixtures/qtl_mini/example_geneexpr.bed.gz","tests/fixtures/qtl_mini/example_covariates.tsv","tests/fixtures/qtl_mini/association_windows.bed"],"outputs":["tests/fixtures/tensorqtl/expected/cis_qtl.pairs.tsv.gz","tests/fixtures/tensorqtl/expected/cis_qtl.regional.tsv.gz"],"files":["tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bed","tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bim","tests/fixtures/qtl_mini/protocol_example.genotype.chr22.fam","tests/fixtures/qtl_mini/example_geneexpr.bed.gz","tests/fixtures/qtl_mini/example_covariates.tsv","tests/fixtures/qtl_mini/association_windows.bed","tests/fixtures/tensorqtl/expected/cis_qtl.pairs.tsv.gz","tests/fixtures/tensorqtl/expected/cis_qtl.regional.tsv.gz"]},"bulk_expression_QC":{"dir":"tests/fixtures/bulk_expression_normalization","dirs":["tests/fixtures/bulk_expression_normalization","tests/fixtures/bulk_expression_normalization/expected"],"inputs":["tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.geneCount.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.sample_participant_lookup.txt"],"outputs":["tests/fixtures/bulk_expression_normalization/expected/expected.qc_1.low_expression_filtered.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_2.outlier_removed.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_3.outlier_removed.geneCount.gct.gz"],"files":["tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.geneCount.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.sample_participant_lookup.txt","tests/fixtures/bulk_expression_normalization/expected/expected.qc_1.low_expression_filtered.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_2.outlier_removed.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_3.outlier_removed.geneCount.gct.gz"]},"mnm_regression":{"dir":"tests/fixtures/mnm_regression","dirs":["tests/fixtures/mnm_regression/expected"],"inputs":[],"outputs":["tests/fixtures/mnm_regression/expected/univariate_bvsr.rds","tests/fixtures/mnm_regression/expected/univariate_twas_weights.rds"],"files":["tests/fixtures/mnm_regression/expected/univariate_bvsr.rds","tests/fixtures/mnm_regression/expected/univariate_twas_weights.rds"]}},PREVIEWS={"tests/fixtures/gwas_qc/protocol_example.pheno.bed":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","1","2","G1","0.1","0.1","0.1","0.1"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/gwas_qc/protocol_example.kin0":{"kind":"table","rows":[["#FID1","IID1","FID2","IID2","NSNP","HETHET","IBS0","KINSHIP"],["0","SAMPLE_019","0","SAMPLE_008","3017","0.0775605","0.0215446","0.0713166"],["0","SAMPLE_038","0","SAMPLE_002","2966","0.0795684","0.0229265","0.062709"],["0","SAMPLE_040","0","SAMPLE_002","2952","0.0785908","0.0254065","0.062986"]],"shownColumns":8,"totalColumns":8,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/king.kin0":{"kind":"table","rows":[["#FID1","IID1","FID2","IID2","NSNP","HETHET","IBS0","KINSHIP"],["0","SAMPLE_019","0","SAMPLE_008","3017","0.0775605","0.0215446","0.0713166"],["0","SAMPLE_038","0","SAMPLE_002","2966","0.0795684","0.0229265","0.062709"],["0","SAMPLE_040","0","SAMPLE_002","2952","0.0785908","0.0254065","0.062986"]],"shownColumns":8,"totalColumns":8,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/king_2.related_id":{"kind":"table","rows":[["0","SAMPLE_038"],["0","SAMPLE_040"],["0","SAMPLE_041"],["0","SAMPLE_048"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/king_split.unrelated.fam":{"kind":"table","rows":[["0","SAMPLE_006","0","0","0","-9"],["0","SAMPLE_007","0","0","0","-9"],["0","SAMPLE_008","0","0","0","-9"],["0","SAMPLE_009","0","0","0","-9"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/king_split.related.fam":{"kind":"table","rows":[["0","SAMPLE_001","0","0","0","-9"],["0","SAMPLE_002","0","0","0","-9"],["0","SAMPLE_003","0","0","0","-9"],["0","SAMPLE_004","0","0","0","-9"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/qc_no_prune.bim":{"kind":"table","rows":[["22","chr22:10685239_C_T","0","10685239","T","C"],["22","chr22:10761227_G_A","0","10761227","A","G"],["22","chr22:11285239_C_T","0","11285239","T","C"],["22","chr22:11601805_G_A","0","11601805","A","G"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/qc_ld_prune.prune.in":{"kind":"table","rows":[["chr22:10761227_G_A"],["chr22:10859684_C_G"],["chr22:11271327_T_C"],["chr22:11285239_C_T"]],"shownColumns":1,"totalColumns":1,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/qc_ld_prune.bim":{"kind":"table","rows":[["22","chr22:10761227_G_A","0","10761227","A","G"],["22","chr22:10859684_C_G","0","10859684","G","C"],["22","chr22:11271327_T_C","0","11271327","C","T"],["22","chr22:11285239_C_T","0","11285239","T","C"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/sample_overlap.txt":{"kind":"table","rows":[["genotype_id","sample_id"],["SAMPLE_001","SAMPLE_001"],["SAMPLE_002","SAMPLE_002"],["SAMPLE_003","SAMPLE_003"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/king_workflow.unrelated.fam":{"kind":"table","rows":[["0","SAMPLE_001","0","0","0","-9"],["0","SAMPLE_002","0","0","0","-9"],["0","SAMPLE_003","0","0","0","-9"],["0","SAMPLE_004","0","0","0","-9"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/pca/protocol_example.pca_pheno.txt":{"kind":"table","rows":[["FID","IID","msex","age_death","pmi","study","race"],["SAMPLE_001","SAMPLE_001","1","90.97","10.57","1","1"],["SAMPLE_002","SAMPLE_002","1","80.24","7.87","0","1"],["SAMPLE_003","SAMPLE_003","1","83.9","9.93","0","1"]],"shownColumns":7,"totalColumns":7,"truncatedColumns":false},"tests/fixtures/pca/expected/project_samples.rds":{"kind":"rds","lines":["Object: list [length 6]"," Components: pca_model, pc_scores, meta, pc_cov, pc_mean, pc_median","$pca_model: flashpca [length 7]"," Components: values, vectors, projection, loadings, center, scale, pve","$pc_scores: data.frame [118 x 28]"," ID FID IID MID PID SEX"," 1 SAMPLE_001:SAMPLE_001 SAMPLE_001 SAMPLE_001 0 0 0"," 2 SAMPLE_002:SAMPLE_002 SAMPLE_002 SAMPLE_002 0 0 0"," 3 SAMPLE_003:SAMPLE_003 SAMPLE_003 SAMPLE_003 0 0 0","","$meta: character [length 1]"," Values: \"protocol_example.unrelated.prune \"","$pc_cov: matrix/array [5 x 5]"," [,1] [,2] [,3] [,4] [,5]"," [1,] 2.723426e-02 8.339899e-19 9.452205e-18 -3.973604e-18 2.797100e-19"," [2,] 8.339899e-19 2.696550e-02 8.385917e-18 9.369324e-18 2.240701e-17"," [3,] 9.452205e-18 8.385917e-18 2.612153e-02 1.781369e-17 -1.472802e-18","","$pc_mean: numeric [length 5]"," Values: c(-8.82062784394987e-18, -3.01077430406822e-17, 2.72851421306183e-17, 1.83469059154157e-17, 4.39855308484967e-17)","$pc_median: numeric [length 5]"," Values: c(0.00602721681627851, -0.00488368656715891, -0.003213717717953, -0.0157996403619344, 0.012215640237604)"]},"tests/fixtures/pca/expected/detect_outliers.maha.rds":{"kind":"rds","lines":["Object: list [length 4]"," Components: pc, manh_dis_sq_cutoff, msg, outliers","$pc: data.frame [59 x 25]"," IID FID pop PC1 PC2 PC3"," 1 SAMPLE_001 SAMPLE_001 1 -0.01226109 -0.07562966 -0.06502774"," 2 SAMPLE_002 SAMPLE_002 1 -0.27276569 -0.13080698 0.02576653"," 3 SAMPLE_003 SAMPLE_003 1 -0.01342011 -0.05296450 0.01199865","","$manh_dis_sq_cutoff: numeric [length 1]"," Values: c(`97.5%` = 12.1527505435543)","$msg: character [length 1]"," Values: \"# protocol_example.unrelated.prune result summary\\n## Mahalanobis distance summary:\\n```\\n Min. 1st Qu. Median Mean 3rd Qu. Max. \\n 0.2622 2.9169 4.2592 4.9153 6.5099 15.5199 \\n```\\n The cut-off for outlier removal is set to: 12.1527505435543 and the number of individuals to remove is: 2 \\n The new sample size after outlier removal is: 57 \\n\"","$outliers: data.frame [2 x 2]"," FID IID"," 40 SAMPLE_040 SAMPLE_040"," 51 SAMPLE_051 SAMPLE_051"]},"tests/fixtures/pca/expected/detect_outliers.outliers.txt":{"kind":"table","rows":[["SAMPLE_040","SAMPLE_040"],["SAMPLE_051","SAMPLE_051"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/pca/expected/pca_plink.eigenvec":{"kind":"table","rows":[["#FID","IID","PC1","PC2","PC3","PC4","PC5","PC6"],["SAMPLE_001","SAMPLE_001","0.00975568","0.0604747","-0.0528306","-0.0341157","0.0780374","0.193927"],["SAMPLE_002","SAMPLE_002","0.217029","0.104595","0.0209335","-0.132771","-0.0285064","-0.188891"],["SAMPLE_003","SAMPLE_003","0.0106779","0.0423513","0.00974808","0.0217471","-0.246944","-0.16355"]],"shownColumns":8,"totalColumns":22,"truncatedColumns":true},"tests/fixtures/pca/expected/flashpca.eigenvalues.tsv":{"kind":"table","rows":[["component","value","pve"],["1","1.57958724525007","0.0268867862620996"],["2","1.56399922939302","0.0266214564097226"],["3","1.51504853915088","0.0257882471331346"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/rna_calling/protocol_example.rnaseq.fastq.list.txt":{"kind":"table","rows":[["ID","fq1","fq2","strand","read_length"],["SAMPLE_001","SAMPLE_001_R1.fastq.gz","SAMPLE_001_R2.fastq.gz","rf","100"],["SAMPLE_002","SAMPLE_002_R1.fastq.gz","SAMPLE_002_R2.fastq.gz","rf","100"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/rna_calling/SAMPLE_001.rnaseqc.metrics.tsv":{"kind":"table","rows":[["Sample","SAMPLE_001"],["Mapping Rate","0.95"],["Genes Detected","2"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/rna_calling/SAMPLE_002.rnaseqc.metrics.tsv":{"kind":"table","rows":[["Sample","SAMPLE_002"],["Mapping Rate","0.95"],["Genes Detected","3"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/susie_enloc/protocol_example.enloc.gwas_meta.tsv":{"kind":"table","rows":[["#chr","start","end","region_id","TSS","original_data","combined_data","combined_data_sumstats"],["chr1","17351816","20110062","chr1_17351816_20110062","NA","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_17351816_20110062.univariate_susie_rss.rds","protocol_example.enloc.gwas.chr1_17351816_20110062.cis_results_db.export.rds","protocol_example.enloc.gwas.chr1_17351816_20110062.cis_results_db.export_sumstats.rds"],["chr1","20110062","22020160","chr1_20110062_22020160","NA","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_20110062_22020160.univariate_susie_rss.rds","protocol_example.enloc.gwas.chr1_20110062_22020160.cis_results_db.export.rds","protocol_example.enloc.gwas.chr1_20110062_22020160.cis_results_db.export_sumstats.rds"],["chr1","22020160","24199848","chr1_22020160_24199848","NA","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds","protocol_example.enloc.gwas.chr1_22020160_24199848.cis_results_db.export.rds","protocol_example.enloc.gwas.chr1_22020160_24199848.cis_results_db.export_sumstats.rds"]],"shownColumns":8,"totalColumns":11,"truncatedColumns":true},"tests/fixtures/susie_enloc/protocol_example.enloc.xqtl_meta.tsv":{"kind":"table","rows":[["#chr","start","end","region_id","TSS","original_data","combined_data","combined_data_sumstats"],["chr1","20520000","24080000","ENSG00000142798","21937309","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds,protocol_example.enloc.KNIGHT_pQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.qtl.ENSG00000142798.cis_results_db.export.rds","protocol_example.enloc.qtl.ENSG00000142798.cis_results_db.export_sumstats.rds"]],"shownColumns":8,"totalColumns":13,"truncatedColumns":true},"tests/fixtures/susie_enloc/expected/coloc.rds":{"kind":"rds","lines":["Object: data.frame [120 x 17]"," study context trait method gwasStudy gwasMethod"," 1 MiGA_eQTL MiGA_GFM_eQTL ENSG00000142798 susie AD_Bellenguez_2022 susie_rss"," 2 MiGA_eQTL MiGA_GFM_eQTL ENSG00000142798 susie AD_Bellenguez_2022 susie_rss"," 3 MiGA_eQTL MiGA_GFM_eQTL ENSG00000142798 susie AD_Bellenguez_2022 susie_rss"]},"tests/fixtures/susie_enloc/expected/colocboost.rds":{"kind":"rds","lines":["Object: list [length 4]"," Components: xqtl_coloc, joint_gwas, separate_gwas, computing_time","$xqtl_coloc: colocboost [length 6]"," Components: cos_summary, vcp, cos_details, data_info, model_info, ucos_details","$joint_gwas: NULL [length 0]","$separate_gwas: NULL [length 0]","$computing_time: list [length 1]"," Components: Analysis"]},"tests/fixtures/susie_enloc/expected/colocboost_manifest.tsv":{"kind":"table","rows":[["region_id","gene_id","chr","start","end","ld_block","studies","gwas_tsvs"],["ENSG00000283047","ENSG00000283047","chr22","10439387","11461338","chr22:10439387-11461338","",""]],"shownColumns":8,"totalColumns":12,"truncatedColumns":true},"tests/fixtures/susie_enloc/expected/enloc_manifest.enrichment.tsv":{"kind":"table","rows":[["unit_id","qtl_files","gwas_files"],["MiGA_GTS_eQTL","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds"],["MiGA_SVZ_eQTL","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds"],["MiGA_THA_eQTL","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/susie_enloc/expected/enloc_manifest.coloc.tsv":{"kind":"table","rows":[["unit_id","qtl_files","gwas_files"],["MiGA_GTS_eQTL@ENSG00000142798","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds"],["MiGA_SVZ_eQTL@ENSG00000142798","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds"],["MiGA_THA_eQTL@ENSG00000142798","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/vcf_qc/numeric_chr22.vcf.gz":{"kind":"table","rows":[["##fileformat=VCFv4.2"],["##FILTER="],["##fileDate=20231023"],["##source=PLINKv1.90"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/vcf_qc/genotype.chr22_48M.vcf.gz":{"kind":"table","rows":[["##fileformat=VCFv4.2"],["##FILTER="],["##fileDate=20231023"],["##source=PLINKv1.90"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/vcf_qc/expected/rename_chrs.variants.tsv":{"kind":"table","rows":[["chr22","10526333","chr22:10526333_CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT_*","CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT","*"],["chr22","10526566","chr22:10526566_AC_*","AC","*"],["chr22","10657618","chr22:10657618_C_G","C","G"],["chr22","10684490","chr22:10684490_G_A","G","A"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/vcf_qc/expected/qc_normalize.variants.tsv":{"kind":"table","rows":[["chr22","48000321","chr22:48000321:GT:G","GT","G"],["chr22","48000321","chr22:48000321:G:GTT","G","GTT"],["chr22","48000321","chr22:48000321:G:GTTT","G","GTTT"],["chr22","48000321","chr22:48000321:G:GTTTT","G","GTTTT"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/vcf_qc/expected/qc_3.novel.tstv":{"kind":"table","rows":[["TS/TV","stats:"],["No","results","available","(empty","input?)"],["Hom/Het","stats:"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/vcf_qc/expected/qc_3.known.tstv":{"kind":"table","rows":[["TS/TV stats:"],["Sample ","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["Transitions ","28","23","23","20","24","24","27"],["Transversions ","4","5","4","4","4","5","6"]],"shownColumns":8,"totalColumns":62,"truncatedColumns":true},"tests/fixtures/apa_calling/depth.txt":{"kind":"table","rows":[["SAMPLE_001","12709"],["SAMPLE_002","14497"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/apa_calling/chr22_3UTR.bed":{"kind":"table","rows":[["chr22","16654066","16654076","ENST00000456726|NA|chr22|-","0","-"],["chr22","16669464","16669620","ENST00000457060|ANKRD62P1-PARP4P3|chr22|-","0","-"],["chr22","17116297","17121360","ENST00000331437|TMEM121B|chr22|-","0","-"],["chr22","17116299","17120143","ENST00000399875|TMEM121B|chr22|-","0","-"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/apa_calling/chr22.hdr.gtf.gz":{"kind":"table","rows":[["#!header1"],["#!header2"],["#!header3"],["#!header4"]],"shownColumns":1,"totalColumns":1,"truncatedColumns":false},"tests/fixtures/apa_impute/protocol_example.apa_matchtable.txt":{"kind":"table","rows":[["ProjID","SampleID"],["Sample001","SampleA"],["Sample002","SampleB"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/apa_impute/apa_chr22/Dapars_result_result_temp.chr22.txt":{"kind":"table","rows":[["Gene","fit_value","Predicted_Proximal_APA","Loci","output/apa/wig/SAMPLE_001_PDUI","output/apa/wig/SAMPLE_002_PDUI"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/apa_impute/expected/expected.Dapars_result_impute_chr22.bed":{"kind":"table","rows":[["#chr","start","end","Gene"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/apa_impute/expected/expected.Dapars_allchrom.bed":{"kind":"table","rows":[["#chr","start","end","Gene"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/apa_impute/expected/expected.Dapars_result_impute_renamed_chr22.bed.gz":{"kind":"table","rows":[["#chr","start","end","Gene"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/apa_impute/expected/expected.Dapars_allchrom_renamed.bed":{"kind":"table","rows":[["#chr","start","end","Gene"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.tpm.gct.gz":{"kind":"table","rows":[["#1.2"],["# 300 60 "],["gene_ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","4.46908614068004","3.6324384389436","0","0.926449274182614","8.44864560635242","16.3456237133014","4.07740959667351"]],"shownColumns":8,"totalColumns":61,"truncatedColumns":true},"tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.geneCount.gct.gz":{"kind":"table","rows":[["#1.2"],["# 300 60 "],["gene_ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","197","193","122","180","217","257","195"]],"shownColumns":8,"totalColumns":61,"truncatedColumns":true},"tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.sample_participant_lookup.txt":{"kind":"table","rows":[["sample_id","participant_id"],["SAMPLE_001","SAMPLE_001"],["SAMPLE_002","SAMPLE_002"],["SAMPLE_003","SAMPLE_003"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/bulk_expression_normalization/expected/expected.qc_1.low_expression_filtered.tpm.gct.gz":{"kind":"table","rows":[["#1.2"],["# 300 60"],["gene_ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","4.46908614068004","3.6324384389436","0","0.926449274182614","8.44864560635242","16.3456237133014","4.07740959667351"]],"shownColumns":8,"totalColumns":61,"truncatedColumns":true},"tests/fixtures/bulk_expression_normalization/expected/expected.qc_2.outlier_removed.tpm.gct.gz":{"kind":"table","rows":[["#1.2"],["# 300 54"],["gene_ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","4.46908614068004","3.6324384389436","0","0.926449274182614","8.44864560635242","16.3456237133014","4.07740959667351"]],"shownColumns":8,"totalColumns":55,"truncatedColumns":true},"tests/fixtures/bulk_expression_normalization/expected/expected.qc_3.outlier_removed.geneCount.gct.gz":{"kind":"table","rows":[["#1.2"],["# 300 54 "],["gene_ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","197","193","122","180","217","257","195"]],"shownColumns":8,"totalColumns":55,"truncatedColumns":true},"tests/fixtures/colocboost/expected/test_coloc.ENSG00000283047.colocboost.rds":{"kind":"rds","lines":["Object: list [length 4]"," Components: xqtl_coloc, joint_gwas, separate_gwas, computing_time","$xqtl_coloc: colocboost [length 6]"," Components: cos_summary, vcp, cos_details, data_info, model_info, ucos_details","$joint_gwas: NULL [length 0]","$separate_gwas: NULL [length 0]","$computing_time: list [length 1]"," Components: Analysis"]},"tests/fixtures/covariate_formatting/covariates.base.tsv":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","1","1","0","0"],["age","90.97","80.24","83.9","74.1","93.94","89.95","91.39"]],"shownColumns":8,"totalColumns":61,"truncatedColumns":true},"tests/fixtures/covariate_formatting/expected/merged.gz":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","1","1","0","0"],["age","90.97","80.24","83.9","74.1","93.94","89.95","91.39"],["PC1","-0.012261092152600217","-0.27276568851005745","-0.013420106161445802","0.11884720720763796","0.006027216816278508","0.16975817747495048","-0.176420328093058"]],"shownColumns":8,"totalColumns":60,"truncatedColumns":true},"tests/fixtures/covariate_hidden_factor/covariates.tsv":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","0","1","0","1"],["age","67.06","82.92","87.76","64.57","81.62","66.44","75.53"],["PC1","-0.7904","-0.1993","0.3059","2.1952","-0.0345","-0.4571","0.7942"]],"shownColumns":8,"totalColumns":50,"truncatedColumns":true},"tests/fixtures/covariate_hidden_factor/expected/residual.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","10939387","10961337","ENSG00000283047","29.946170491386496","-8.44968773314525","-1.7767246013041644","-3.7499243841617105"],["chr22","15528191","15529138","ENSG00000130538","-2.9173358185760385","-5.007200781431884","-0.29519619760879173","3.938154273806503"],["chr22","15611758","15613095","ENSG00000231565","2.85916554775662","-4.676226628425212","-1.6400806273227975","2.675546611283106"]],"shownColumns":8,"totalColumns":53,"truncatedColumns":true},"tests/fixtures/covariate_hidden_factor/expected/Marchenko_PC.gz":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","0","1","0","1"],["age","67.06","82.92","87.76","64.57","81.62","66.44","75.53"],["PC1","-0.7904","-0.1993","0.3059","2.1952","-0.0345","-0.4571","0.7942"]],"shownColumns":8,"totalColumns":50,"truncatedColumns":true},"tests/fixtures/covariate_hidden_factor/expected/Buja_Eyuboglu_PC.gz":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","0","1","0","1"],["age","67.06","82.92","87.76","64.57","81.62","66.44","75.53"],["PC1","-0.7904","-0.1993","0.3059","2.1952","-0.0345","-0.4571","0.7942"]],"shownColumns":8,"totalColumns":50,"truncatedColumns":true},"tests/fixtures/covariate_hidden_factor/expected/PEER.factors.tsv":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["Factor1","-1.9689868302480802","-0.5777142629714919","-1.1097844168668152","-0.31776012143574744","0.9316883100761433","0.461826912428385","1.2043828829636531"],["Factor2","0.4928233935806234","-0.08549472177185433","0.8183972887349434","-0.9338565272256283","-0.6584489418683644","-0.4483268381001687","1.823597083931354"],["Factor3","0.3501340710245686","0.14571533939177014","-0.5173588766334256","-0.292175817326537","0.8664977538348799","1.1397705268157454","-0.10010811198261901"]],"shownColumns":8,"totalColumns":50,"truncatedColumns":true},"tests/fixtures/covariate_hidden_factor/expected/PEER.weights.tsv":{"kind":"table","rows":[["feature","Factor1","Factor2","Factor3","Factor4","Factor5"],["ENSG00000283047","-1.7436415740900164","0.2583746743255404","0.47822872128514793","0.5615754310448298","-0.9215818059252844"],["ENSG00000130538","-0.049466108478791494","0.38421328122758064","0.2847230657691795","-0.5102580319457181","0.45561780188119266"],["ENSG00000231565","-0.008886816628110559","-0.466616472403423","0.5875801940739112","-0.3895713470241593","0.15342578346522723"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/covariate_hidden_factor/expected/PEER.variance.tsv":{"kind":"table","rows":[["factor","r2"],["Factor1","3.361230579495944"],["Factor2","3.297627272191017"],["Factor3","2.536700993320218"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/covariate_hidden_factor/expected/PEER.gz":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","0","1","0","1"],["age","67.06","82.92","87.76","64.57","81.62","66.44","75.53"],["PC1","-0.7904","-0.1993","0.3059","2.1952","-0.0345","-0.4571","0.7942"]],"shownColumns":8,"totalColumns":50,"truncatedColumns":true},"tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr1.tsv":{"kind":"table","rows":[["variant_id","gnomad_MAF"],["chr1:1000:C:G","0.14834847690550854"],["chr1:1037:A:T","0.4960064205828956"],["chr1:1074:A:G","0.12478507852411996"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr2.tsv":{"kind":"table","rows":[["variant_id","gnomad_MAF"],["chr2:1000:T:T","0.24893867622188837"],["chr2:1037:A:A","0.2905828566430643"],["chr2:1074:G:C","0.12085436431595521"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/ems_training/model_config.yaml":{"kind":"table","rows":[["#","Toy","model","configuration","for","EMS","training/prediction","MWE"],["system:"],["temp_directory:","\"/tmp/ems_dask\""],["random_seeds:"]],"shownColumns":8,"totalColumns":8,"truncatedColumns":false},"tests/fixtures/ems_training/expected/features_importance_model5_chr_chr2_NPR_1.csv":{"kind":"table","rows":[["feature","importance"],["chrombpnet_positive","25.262471700633572"],["tf_positive","14.94907294258858"],["gnomad_MAF","14.039430745796125"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/ems_training/expected/model_5_summary_chr_chr2_NPR_1.json":{"kind":"table","rows":[["{\"CatBoost\":{\"standard_subset_weighted\":{\"AP_test\":0.49887492","AUC_test:0.50612204","params:{\"iterations\":50","depth:4","learning_rate:0.1","loss_function:\"Logloss\"","random_seed:0","logging_level:\"Silent\""]],"shownColumns":8,"totalColumns":38,"truncatedColumns":true},"tests/fixtures/ems_training/expected/predictions_weighted_model_chr2.tsv":{"kind":"table","rows":[["variant_id","gene_id","CHR","BP","REF","ALT","SNP","pip"],["chr1:1000:C:G","ENSG00000100019","1","1000","C","G","chr1:1000:C:G","0.2817534630608156"],["chr1:1037:A:T","ENSG00000100035","1","1037","A","T","chr1:1037:A:T","0.68284686124174"],["chr1:1074:A:G","ENSG00000100036","1","1074","A","G","chr1:1074:A:G","0.24044852098155267"]],"shownColumns":8,"totalColumns":28,"truncatedColumns":true},"tests/fixtures/eoo_enrichment/protocol_example.eoo_baseline_annotation.tsv.gz":{"kind":"table","rows":[["chr","BP","ref","alt","rsid","maf","ANNO_baseline"],["1","10000654","A","C","rs1_0","0.3734","0"],["1","10100228","C","T","rs1_1","0.0602","0"],["1","10200604","T","A","rs1_2","0.0246","0"]],"shownColumns":7,"totalColumns":7,"truncatedColumns":false},"tests/fixtures/eoo_enrichment/protocol_example.eoo_significant_variants.tsv.gz":{"kind":"table","rows":[["chr","pos"],["1","100015157"],["1","1000291"],["1","100065691"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/eoo_enrichment/expected/enrichment_results.rds":{"kind":"rds","lines":["Object: list [length 10]"," Components: summary, OR_blockJacknife, Enrichment_blockJacknife, OR, Enrichment, OR_sd, Enrichment_sd, Enrichment_Z_scores, ...","$summary: data.frame [2 x 13]"," Annotation OR OR_SE OR_log2 OR_SE_log2 Enrichment"," maf maf 1 0 0 0 1"," ANNO_baseline ANNO_baseline 1 0 0 0 1","","$OR_blockJacknife: matrix/array [22 x 2]"," maf ANNO_baseline"," [1,] 1 1"," [2,] 1 1"," [3,] 1 1","","$Enrichment_blockJacknife: matrix/array [22 x 2]"," maf ANNO_baseline"," [1,] 1 1"," [2,] 1 1"," [3,] 1 1","","$OR: numeric [length 2]"," Values: c(maf = 0, ANNO_baseline = 0)","$Enrichment: numeric [length 2]"," Values: c(maf = 1, ANNO_baseline = 1)","$OR_sd: numeric [length 2]"," Values: c(0, 0)"]},"tests/fixtures/eoo_enrichment/expected/enrichment_results_summary.tsv.gz":{"kind":"table","rows":[["Annotation","OR","OR_SE","OR_log2","OR_SE_log2","Enrichment","Enrichment_SE","Enrichment_log2"],["maf","1","0","0","0","1","0","0"],["ANNO_baseline","1","0","0","0","1","0","0"]],"shownColumns":8,"totalColumns":13,"truncatedColumns":true},"tests/fixtures/gene_annotation/protocol_example.atac.tsv":{"kind":"table","rows":[["ID","S0561","S0321","S1177","S1098","S1252","S1170","S0634"],["C22P107555","2.65660494706228","2.96635134658411","2.28130807122782","1.98238696298197","2.32521464070871","3.3786450787504","3.25578026613787"],["C22P107557","2.80449305810594","3.56480978765153","2.8300407115426","3.42626771666669","2.79542295970582","3.20668973364495","3.29702988602781"],["C22P107559","3.62969398452243","3.54653724981745","3.46664752019843","3.68920172704657","3.43819373054703","3.14576639188727","3.2703678752323"]],"shownColumns":8,"totalColumns":11,"truncatedColumns":true},"tests/fixtures/gene_annotation/protocol_example.rnaseq.bed.gz":{"kind":"table","rows":[["gene_id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","4.46908614068004","3.6324384389436","0","0.926449274182614","8.44864560635242","16.3456237133014","4.07740959667351"],["ENSG00000273342","0","19.892726241898","13.6287618206549","28.5428919916226","10.1099209273507","17.0947587639983","0"],["ENSG00000128274","28.6051391056338","18.1638378952795","0","0.282770008563753","0","0","0.961627662095183"]],"shownColumns":8,"totalColumns":61,"truncatedColumns":true},"tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","strand","SAMPLE_001","SAMPLE_002","SAMPLE_003"],["chr22","10939387","10961337","ENSG00000283047","-","37.0768403309204","0","5.5832744229102"],["chr22","15528191","15529138","ENSG00000130538","+","0","1.08358035439567","8.91397741376836"],["chr22","15611758","15613095","ENSG00000231565","-","5.97808406328782","0","2.63711285656005"]],"shownColumns":8,"totalColumns":65,"truncatedColumns":true},"tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.gene_list.tsv":{"kind":"table","rows":[["#chr","start","end","gene_id","strand","gene_name"],["chr22","19146992","19150291","ENSG00000063515","-","GSC2"],["chr22","46267960","46294007","ENSG00000075234","+","TTC38"],["chr22","46360833","46537619","ENSG00000075275","-","CELSR1"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.region_list.txt":{"kind":"table","rows":[["#chr","start","end","ID","strand","path"],["chr22","10939387","10961337","ENSG00000283047","-","protocol_example.rnaseq.bed.bed.gz"],["chr22","15528191","15529138","ENSG00000130538","+","protocol_example.rnaseq.bed.bed.gz"],["chr22","15611758","15613095","ENSG00000231565","-","protocol_example.rnaseq.bed.bed.gz"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","gene_name","SAMPLE_001","SAMPLE_002","SAMPLE_003"],["chr22","17592135","17628748","ENSG00000131100_P36543","ENSG00000131100","-2.13239682163646","0.122048029453446","-0.978243368936795"],["chr22","17787648","18024560","ENSG00000243156_Q7RTP6","ENSG00000243156","-1.98683058179618","-2.381935629468","0.506516811334827"],["chr22","20707690","20859416","ENSG00000241973_P42356","ENSG00000241973","-2.53078001781622","1.810765636291","0.607220843471353"]],"shownColumns":8,"totalColumns":65,"truncatedColumns":true},"tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.gene_list.tsv":{"kind":"table","rows":[["#chr","start","end","gene_id","strand","gene_name"],["chr22","21759656","21867679","ENSG00000100030","-","MAPK1"],["chr22","38483437","38507659","ENSG00000100201","-","DDX17"],["chr22","50343303","50445089","ENSG00000100239","+","PPP6R2"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.region_list.txt":{"kind":"table","rows":[["#chr","start","end","ID","path"],["chr22","17592135","17628748","ENSG00000131100_P36543","protocol_example.protein.no_coord.bed.gz"],["chr22","17787648","18024560","ENSG00000243156_Q7RTP6","protocol_example.protein.no_coord.bed.gz"],["chr22","20707690","20859416","ENSG00000241973_P42356","protocol_example.protein.no_coord.bed.gz"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.atac.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","S0561","S0321","S1177","S1098"],["22","10662152","10664678","C22P107555","2.65660494706228","2.96635134658411","2.28130807122782","1.98238696298197"],["22","16094161","16096165","C22P107557","2.80449305810594","3.56480978765153","2.8300407115426","3.42626771666669"],["22","16110745","16113398","C22P107559","3.62969398452243","3.54653724981745","3.46664752019843","3.68920172704657"]],"shownColumns":8,"totalColumns":14,"truncatedColumns":true},"tests/fixtures/gene_annotation/expected/protocol_example.atac.region_list.txt":{"kind":"table","rows":[["#chr","start","end","ID","path"],["22","10662152","10664678","C22P107555","protocol_example.atac.bed.gz"],["22","16094161","16096165","C22P107557","protocol_example.atac.bed.gz"],["22","16110745","16113398","C22P107559","protocol_example.atac.bed.gz"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.intron_count.tsv.leafcutter.clusters_to_genes.txt":{"kind":"table","rows":[["clu","genes"],["22:clu_10_+","ENSG00000236052"],["22:clu_11_-","ENSG00000185264"],["22:clu_12_-","ENSG00000183765"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.phenotype.bed.formated.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","16675539","16675540","22:16671178:16671518:clu_27_-:ENSG00000189295","0.3150","0.7467","0.4984","0.0886"],["chr22","16675539","16675540","22:16671588:16673600:clu_27_-:ENSG00000189295","0.8687","0.8932","0.4067","0.9612"],["chr22","16675539","16675540","22:16673752:16675123:clu_27_-:ENSG00000189295","0.6683","0.9086","0.4975","0.4455"]],"shownColumns":8,"totalColumns":24,"truncatedColumns":true},"tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.phenotype.bed.phenotype_group.txt":{"kind":"table","rows":[["ID","gene"],["22:16671178:16671518:clu_27_-:ENSG00000189295","ENSG00000189295"],["22:16671178:16671518:clu_27_-:ENSG00000259271","ENSG00000259271"],["22:16671588:16673600:clu_27_-:ENSG00000189295","ENSG00000189295"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.psichomics.phenotype.formated.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","15750824","15750825","SE_51_ENSG00000235992","0.8639","0.0875","0.6938","0.0321"],["chr22","15855242","15855243","SE_29_ENSG00000215270","0.4620","0.4195","0.6668","0.0903"],["chr22","16659627","16659628","SE_8_ENSG00000249263","0.3273","0.9916","0.5155","0.9725"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/gene_annotation/expected/protocol_example.psichomics.phenotype.phenotype_group.txt":{"kind":"table","rows":[["SE_51_ENSG00000235992","ENSG00000235992_SE"],["SE_29_ENSG00000215270","ENSG00000215270_SE"],["SE_8_ENSG00000249263","ENSG00000249263_SE"],["SE_26_ENSG00000259271","ENSG00000259271_SE"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/generalized_TADB/protocol_example.brain_TADs.txt":{"kind":"table","rows":[["chr22","10700000","12700000"],["chr22","10750000","12650000"],["chr22","13000000","15000000"],["chr22","15200000","17200000"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/generalized_TADB/protocol_example.gene_start_end.tsv":{"kind":"table","rows":[["","#chr","start","end","gene_id","gene_name"],["1","chr22","10736171","10736283","ENSG00000277248","U2"],["2","chr22","10939388","10961338","ENSG00000283047","FRG1FP"],["3","chr22","11066417","11068174","ENSG00000279973","CU104787.1"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/generalized_TADB/expected/generalized_TAD.tsv":{"kind":"table","rows":[["chr22","10700000","12700000"],["chr22","13000000","15000000"],["chr22","15200000","17200000"],["chr22","17500000","19500000"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/generalized_TADB/expected/generalized_TADB.tsv":{"kind":"table","rows":[["#chr","start","end","index"],["chr22","0","13000000","TADB1"],["chr22","12650000","15300000","TADB2"],["chr22","15000000","17500000","TADB3"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/generalized_TADB/expected/TADB_enhanced_cis.bed":{"kind":"table","rows":[["#chr","start","end","gene_id"],["chr22","0","13000000","ENSG00000226444"],["chr22","0","13000000","ENSG00000276871"],["chr22","0","13000000","ENSG00000277248"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/generalized_TADB/expected/extended_TADB.bed":{"kind":"table","rows":[["#chr","start","end","index"],["chr22","0","13626642","TADB_1"],["chr22","12650000","16304556","TADB_2"],["chr22","14273854","18558149","TADB_3"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/genotype_formatting/geno/chr21.bim":{"kind":"table","rows":[["21","chr21:5091891_A_G","0","5091891","G","A"],["21","chr21:5097593_CGTCCCTTCCCGAGGTTCCAGGCGGACGT_C","0","5097593","C","CGTCCCTTCCCGAGGTTCCAGGCGGACGT"],["21","chr21:5097593_CGTCCCTTCCCGAGGTTCCAGGCGGACGT_CGTCCCTTCCCGAGGTTCCAGGCGGACGTGTCCCTTCCCGAGGTTCCAGGCGGACGT","0","5097593","CGTCCCTTCCCGAGGTTCCAGGCGGACGTGTCCCTTCCCGAGGTTCCAGGCGGACGT","CGTCCCTTCCCGAGGTTCCAGGCGGACGT"],["21","chr21:5097593_CGTCCCTTCCCGAGGTTCCAGGCGGACGT_TGTCCCTTCCCGAGGTTCCAGGCGGACGT","0","5097593","TGTCCCTTCCCGAGGTTCCAGGCGGACGT","CGTCCCTTCCCGAGGTTCCAGGCGGACGT"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/genotype_formatting/expected/ld_by_region.float16.rds":{"kind":"rds","lines":["Object: list [length 2]"," Components: ld, variant_ids","$ld: matrix/array [75 x 75]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] NaN 0 0 0 0 0"," [2,] NaN 1 0 0 0 0"," [3,] NaN NaN NaN 0 0 0","","$variant_ids: character [length 75]"," Values: c(\"chr22:16051446_C_A\", \"chr22:16054534_GCAAAGTGATC_G\", \"chr22:16054534_GCAAAGTGATC_TCAAAGTGATC\", \"chr22:16054540_T_*\", \"chr22:16054540_T_C\", \"chr22:16059969_T_A\" ) ..."]},"tests/fixtures/genotype_formatting/expected/plink_to_vcf.variants.tsv":{"kind":"table","rows":[["chr22","10526333","chr22:10526333_CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT_*","CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT","*"],["chr22","10526566","chr22:10526566_AC_*","AC","*"],["chr22","10657618","chr22:10657618_C_G","C","G"],["chr22","10684490","chr22:10684490_G_A","G","A"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/genotype_formatting/expected/vcf_to_plink.bim":{"kind":"table","rows":[["22","chr22:10526333_CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT_*","0","10526333","*","CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT"],["22","chr22:10526566_AC_*","0","10526566","*","AC"],["22","chr22:10657618_C_G","0","10657618","G","C"],["22","chr22:10684490_G_A","0","10684490","A","G"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/genotype_formatting/expected/genotype_by_region.bim":{"kind":"table","rows":[["chr22","chr22:16022590_G_T","0","16022590","T","G"],["chr22","chr22:16022788_G_T","0","16022788","T","G"],["chr22","chr22:16024185_G_A","0","16024185","A","G"],["chr22","chr22:16025239_GACAA_G","0","16025239","G","GACAA"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/genotype_formatting/expected/genotype_by_chrom.bim":{"kind":"table","rows":[["22","chr22:10526333_CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT_*","0","10526333","*","CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT"],["22","chr22:10526566_AC_*","0","10526566","*","AC"],["22","chr22:10657618_C_G","0","10657618","G","C"],["22","chr22:10684490_G_A","0","10684490","A","G"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gregor/index.snps.txt":{"kind":"table","rows":[["22:19449483"],["22:41441787"],["22:39507863"],["22:29485708"]],"shownColumns":1,"totalColumns":1,"truncatedColumns":false},"tests/fixtures/gregor/test_peaks.bed":{"kind":"table","rows":[["chr22","19449433","19449533","."],["chr22","29485658","29485758","."]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/gregor/example_enrichment_results.txt":{"kind":"table","rows":[["Bed_File","InBed_Index_SNP","ExpectNum_of_InBed_SNP","PValue","N1_N2","Np","Np_Nn","odds"],["test_peaks.bed","1","0.4","0.880024175924493","2","4","30","7.35976894209104"],["other_peaks.bed","3","1.2","0.5","6","30","90","2.10"]],"shownColumns":8,"totalColumns":11,"truncatedColumns":true},"tests/fixtures/gregor/expected/enrichment_results.txt":{"kind":"table","rows":[["Bed_File","InBed_Index_SNP","ExpectNum_of_InBed_SNP","PValue","N1_N2","Np","Np_Nn","odds"],["test_peaks.bed","1","0.4","0.880024175924493","2","4","30","7.35976894209104"]],"shownColumns":8,"totalColumns":11,"truncatedColumns":true},"tests/fixtures/gsea/protocol_example.pathway_genes.tsv":{"kind":"table","rows":[["group","gene_id"],["geneset1","ENSG00000141510"],["geneset1","ENSG00000139618"],["geneset1","ENSG00000012048"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/gsea/expected/pathway_go_results.rds":{"kind":"rds","lines":["Object: data.frame [2706 x 17]"," category subcategory ID"," 1 Gene Ontology Biological Process GO:0000075"," 2 Gene Ontology Biological Process GO:0000077"," 3 Gene Ontology Biological Process GO:0000082"," Description GeneRatio BgRatio"," 1 cell cycle checkpoint signaling 3/10 187/18860"," 2 DNA damage checkpoint signaling 3/10 117/18860"," 3 G1/S transition of mitotic cell cycle 3/10 246/18860"]},"tests/fixtures/intact/README.md":{"kind":"table","rows":[["# INTACT integration fixture"],["Tiny hand-authored inputs for the `intact` step of"],["`code/SoS/pecotmr_integration/intact.ipynb`"," which joins PTWAS + fastenloc output"],["and runs the Bioconductor **INTACT** package."]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/intact/protocol_example.ptwas.output":{"kind":"table","rows":[["GENE","STAT","SUBCLASS"],["ENSG00000128272","6.8","0"],["ENSG00000100060","5.9","0"],["ENSG00000100075","-0.8","0"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/intact/expected/intact.rds":{"kind":"rds","lines":["Object: data.frame [5 x 5]"," gene zscore GLCP intact_pip fdr_sig"," 1 ENSG00000128272 6.8 0.95 1.0000000 TRUE"," 2 ENSG00000100060 5.9 0.90 0.9999992 TRUE"," 3 ENSG00000183765 2.1 0.22 0.2599521 FALSE"]},"tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.bim":{"kind":"table","rows":[["22","chr22:10526333_CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT_*","0","10526333","*","CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT"],["22","chr22:10526566_AC_*","0","10526566","*","AC"],["22","chr22:10657618_C_G","0","10657618","G","C"],["22","chr22:10684490_G_A","0","10684490","A","G"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.fam":{"kind":"table","rows":[["0","SAMPLE_001","0","0","0","-9"],["0","SAMPLE_002","0","0","0","-9"],["0","SAMPLE_003","0","0","0","-9"],["0","SAMPLE_004","0","0","0","-9"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/mash/mashr_input.rds":{"kind":"rds","lines":["Object: list [length 9]"," Components: strong.b, strong.s, random.b, random.s, null.b, null.s, strong.z, random.z, ...","$strong.b: matrix/array [17 x 8]"," ALL Ast End Exc Inh Mic"," [1,] 0.2490760 0.1114970 -0.0011690 0.2058550 0.202667 0.1912040"," [2,] 0.0927035 -0.0548178 -0.0848382 -0.0164813 0.152236 0.2678570"," [3,] 0.3317760 -0.0481282 0.0288251 0.3373930 0.235520 0.0615115","","$strong.s: matrix/array [17 x 8]"," ALL Ast End Exc Inh Mic"," [1,] 0.0284034 0.0527114 0.0835386 0.0265783 0.0505712 0.0577236"," [2,] 0.0797889 0.1836720 0.3142610 0.0785934 0.1371430 0.2012280"," [3,] 0.0362086 0.0708372 0.1085490 0.0344021 0.0442136 0.0717070","","$random.b: matrix/array [50 x 8]"," ALL Ast End Exc Inh Mic"," [1,] -0.00798796 -0.0162711 0.0247252 0.000681081 0.0151881 0.02678640"," [2,] 0.02479720 -0.0164770 -0.2460290 -0.003475240 0.1236060 0.00559492"," [3,] 0.03869450 -0.0110320 0.0153863 0.027399300 -0.0412417 0.01414480","","$random.s: matrix/array [50 x 8]"," ALL Ast End Exc Inh Mic"," [1,] 0.0279764 0.0492038 0.0747612 0.0262017 0.0485652 0.0519510"," [2,] 0.0272888 0.0476498 0.0744156 0.0247977 0.0451990 0.0510565"," [3,] 0.0284164 0.0513249 0.0815680 0.0261559 0.0472089 0.0559238","","$null.b: matrix/array [50 x 8]"," ALL Ast End Exc Inh Mic"," [1,] -0.0379178 0.1762690 0.2869070 -0.00898611 -0.0313426 -0.14192800"," [2,] -0.0283940 -0.0179526 -0.0189619 0.00314473 -0.0381750 -0.00009733"," [3,] -0.0339721 -0.0189439 -0.1838430 0.09053870 -0.2164520 -0.04149890","","$null.s: matrix/array [50 x 8]"," ALL Ast End Exc Inh Mic"," [1,] 0.0745909 0.1287650 0.2205520 0.0691947 0.125623 0.1375720"," [2,] 0.0247090 0.0434852 0.0680688 0.0228944 0.042475 0.0481976"," [3,] 0.0804790 0.1346920 0.2214130 0.0735394 0.137780 0.1484620"]},"tests/fixtures/mash/region_strong.rds":{"kind":"rds","lines":["Object: list [length 2]"," Components: bhat, sbhat","$bhat: matrix/array [17 x 8]"," ALL Ast End Exc Inh Mic"," [1,] 0.2490760 0.1114970 -0.0011690 0.2058550 0.202667 0.1912040"," [2,] 0.0927035 -0.0548178 -0.0848382 -0.0164813 0.152236 0.2678570"," [3,] 0.3317760 -0.0481282 0.0288251 0.3373930 0.235520 0.0615115","","$sbhat: matrix/array [17 x 8]"," ALL Ast End Exc Inh Mic"," [1,] 0.0284034 0.0527114 0.0835386 0.0265783 0.0505712 0.0577236"," [2,] 0.0797889 0.1836720 0.3142610 0.0785934 0.1371430 0.2012280"," [3,] 0.0362086 0.0708372 0.1085490 0.0344021 0.0442136 0.0717070"]},"tests/fixtures/mash/Ast_De_Jager_eQTL.tsv":{"kind":"table","rows":[["variant_id","z","pip","cs_95"],["chr22:15528227:A:G","0.980877384590622","0.88470232298132","1"],["chr22:15528295:A:G","0.0285784073543268","0.0310205016518012","1"],["chr22:15528301:A:G","-2.77425597107817","0.00847883833339438","0"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/mash/expected/mash_model.EE.rds":{"kind":"rds","lines":["Object: list [length 3]"," Components: mash_model, vhat_file, prior_file","$mash_model: mash [length 9]"," Components: result, loglik, vloglik, null_loglik, alt_loglik, fitted_g, posterior_weights, alpha, ...","$vhat_file: character [length 1]"," Values: \"vhat.rds\"","$prior_file: character [length 1]"," Values: \"prior.rds\""]},"tests/fixtures/mash_posterior/orig.rds":{"kind":"rds","lines":["Object: list [length 2]"," Components: bhat, sbhat","$bhat: matrix/array [17 x 8]"," ALL Ast End Exc Inh Mic"," mash::mash::var1 0.2490760 0.1114970 -0.0011690 0.2058550 0.202667 0.1912040"," mash::mash::var2 0.0927035 -0.0548178 -0.0848382 -0.0164813 0.152236 0.2678570"," mash::mash::var3 0.3317760 -0.0481282 0.0288251 0.3373930 0.235520 0.0615115","","$sbhat: matrix/array [17 x 8]"," ALL Ast End Exc Inh Mic"," mash::mash::var1 0.0284034 0.0527114 0.0835386 0.0265783 0.0505712 0.0577236"," mash::mash::var2 0.0797889 0.1836720 0.3142610 0.0785934 0.1371430 0.2012280"," mash::mash::var3 0.0362086 0.0708372 0.1085490 0.0344021 0.0442136 0.0717070"]},"tests/fixtures/mash_posterior/posterior.rds":{"kind":"rds","lines":["Object: list [length 2]"," Components: PosteriorMean, PosteriorCov","$PosteriorMean: matrix/array [17 x 8]"," ALL Ast End Exc Inh"," mash::mash::var1 0.17232694 0.17232694 0.1723269 0.17232694 0.17232694"," mash::mash::var2 0.01476307 0.01371301 0.0138452 0.01396853 0.01452357"," mash::mash::var3 0.19616044 0.19612898 0.1961331 0.19616209 0.19614862"," Mic"," mash::mash::var1 0.17232694"," mash::mash::var2 0.01446077"," mash::mash::var3 0.19613361","","$PosteriorCov: array [8 x 8 x 17]"," Values: structure(c(0.000202672673211838, 0.000202672660415168, 0.000202672657334736, 0.000202672667085849, 0.000202672663157249, 0.00020267266205673, 0.000202672660415168, 0.000202672795588284, 0.000202672833044135, 0.000202672685212499, 0.000202672744772269, 0.000202672761456718, 0.000202672657334736, 0.000202672833044135, 0.000202672931435478, 0.000202672691934771, 0.000202672775039266, 0.00020267279831929, 0.000202672667085849, 0.000202672685212499, 0.000202672691934771, 0.000202672674726484, 0.000202672679228567, 0.000202672681630198, 0.000202672663157249, 0.000202672744772269, 0.000202672775039266, 0.000202672679228567, 0.000202672726740776, 0.00020267272864298, 0.00020267266205673, 0.000202672761456718, 0.00020267279831929, 0.000202672681630198, 0.00020267272864298, 0.000202672751774356, 0.00020267265981273, 0.000202672795476713, 0.000202672845787816, 0.000202672686527169, 0.000202672750691565, 0.000202672768665906, 0.000202672661847772, 0.000202672764624715, 0.000202672802739626, 0.000202672682086218, 0.000202672730696178, 0.000202672744313261, 0.000690993805157277, 0.00064588947618887, 0.000640967943391216, 0.000641530067803991, 0.000643924292552219, 0.000643674331326419, 0.000645889476188869, 0.000906337969893488, 0.000660843769945103, 0.000658827651347361, 0.000649775937341229, 0.000650796801674549, 0.000640967943391216, 0.000660843769945103, 0.000946162423800497, 0.000657521735095652, 0.000645922237620323, 0.000647225958350737, 0.00064153006780399, 0.000658827651347361, 0.000657521735095652, 0.00070123653112158, 0.000645684987210976, 0.000646776497020376, 0.000643924292552219, 0.000649775937341229, 0.000645922237620323, 0.000645684987210976, 0.000697969329821666, 0.000644665087109268, 0.000643674331326419, 0.000650796801674549, 0.000647225958350737, 0.000646776497020376, 0.000644665087109268, 0.000700828034552002, 0.000643720389557597, 0.000658795526524022, 0.000657038767921531, 0.000655247701009095, 0.000647192071802993, 0.000648102814940983, 0.000647339097446576, 0.000637165970042156, 0.000629745191532584, 0.000632198400689406, 0.000642953957670517, 0.000641780977968221, 0.000274996475008921, 0.000274597826351489, 0.000274634478875012, 0.000274895102245494, 0.000274774091543306, 0.000274639389100835, 0.000274597826351489, 0.000281431493974582, 0.000280358572781969, 0.000274250357578359, 0.00027708647863036, 0.000280243492112642, 0.000274634478875012, 0.000280358572781969, 0.000280445768474198, 0.000274334023718417, 0.000276786408681874, 0.000279516268320755, 0.000274895102245494, 0.000274250357578359, 0.000274334023718417, 0.000275037883252331, 0.000274652715367439, 0.000274345232213175, 0.000274774091543306, 0.00027708647863036, 0.000276786408681874, 0.000274652715367439, 0.000275789325082154, 0.000276746209238406, 0.000274639389100835, 0.000280243492112642, 0.000279516268320755, 0.000274345232213175, 0.000276746209238406, 0.000279634287359727, 0.000274663578648915, 0.00027967656307664, 0.000279026046564802, 0.000274400449314018, 0.000276548172226491, 0.000278938898877881, 0.00027466945735434, 0.000279538784187142, 0.000278906909591904, 0.000274413868543016, 0.000276500043945783, 0.000278822259304957, 0.000243281632388456, 0.000241795439336516, 0.000241797415180052, 0.000241833578726501, 0.000241815300590824, 0.000241798139468473, 0.000241795439336516, 0.000256479144466209, 0.000251769476880683, 0.000240547077465417, 0.000248787965574156, 0.000252553632148097, 0.000241797415180052, 0.000251769476880683, 0.000260489774022465, 0.000240717005884792, 0.000247849295923747, 0.000251108160206683, 0.000241833578726501, 0.000240547077465417, 0.000240717005884792, 0.000243360339092181, 0.000241059665886509, 0.000240632833846987, 0.000241815300590824, 0.000248787965574156, 0.000247849295923747, 0.000241059665886509, 0.000249068840998951, 0.000248325810003554, 0.000241798139468473, 0.000252553632148097, 0.000251108160206683, 0.000240632833846987, 0.000248325810003554, 0.000254747379551046, 0.000241759272162351, 0.000261187793242159, 0.000258580305127097, 0.000239654693045589, 0.000253542422229809, 0.000259898858496253, 0.000241770756568511, 0.000258761083419835, 0.000256480205151462, 0.00023993022266498, 0.000252076606781728, 0.00025763399641408, 0.0012162150643112, 0.00105841475958492, 0.00099789215580201, 0.00109717070864458, 0.00111027302309506, 0.0011059306632207, 0.00105841475958492, 0.00201090514963266, 0.000890520831266493, 0.00105329284087923, 0.00107480446181259, 0.00106765526207329, 0.000997892155802011, 0.000890520831266493, 0.00272846838468087, 0.0010322026880077, 0.000888460328375229, 0.000936540132388815, 0.00109717070864458, 0.00105329284087923, 0.0010322026880077, 0.00121223562590308, 0.00110349561706699, 0.0011007606837934, 0.00111027302309506, 0.00107480446181259, 0.000888460328375229, 0.00110349561706699, 0.00125554273052434, 0.00112246960708966, 0.0011059306632207, 0.00106765526207329, 0.000936540132388814, 0.0011007606837934, 0.00112246960708966, 0.00124046302930025, 0.00110760396025058, 0.0010713326286195, 0.000897965557158104, 0.00110119992489324, 0.00112808001069332, 0.00111913263565441, 0.00110491159726185, 0.00106597969328927, 0.000947774459845704, 0.00110011731781844, 0.00112025190406249, 0.0011135595100208, 1.51088082811018e-15, 2.19984553031266e-16, -5.78963271964974e-16, 2.0703314394745e-15, -2.32589281542517e-16, -2.98227992799423e-16, 2.19984553031266e-16, 9.61326857415861e-16, -1.7433689389371e-16, 6.27067958414194e-16, -6.95634016799429e-17, -8.94146069778939e-17, -5.78963271964974e-16, -1.7433689389371e-16, 4.59375528933787e-15, -1.65795697336437e-15, 1.88540698345908e-16, 2.41172166792823e-16, 2.0703314394745e-15, 6.27067958414194e-16, -1.65795697336437e-15, 6.83010794287169e-15, -6.67330523084712e-16, -8.55017243819948e-16, -2.32589281542517e-16, -6.95634016799429e-17, 1.88540698345908e-16, -6.67330523084712e-16, 8.82644412311252e-16, 9.78472912801509e-17, -2.98227992799423e-16, -8.94146069778939e-17, 2.41172166792823e-16, -8.55017243819948e-16, 9.78472912801509e-17, 7.82554651622793e-16, 2.0010586931819e-14, 6.03269805938047e-15, -1.60953414520564e-14, 5.72547248121967e-14, -6.5003962690404e-15, -8.32350742726878e-15, -1.51655128732836e-15, -4.57968342961883e-16, 1.21802700153181e-15, -4.33970693474545e-15, 4.9143712845081e-16, 6.29089812368518e-16, 1.08617619551487e-08, -3.9242918512654e-08, -2.8140172440362e-09, -1.57148994844309e-09, 3.16743399688553e-09, 1.11659687239979e-09, -3.9242918512654e-08, 0.00187489135683699, 1.15992321848839e-08, 6.47763140550062e-09, -1.30560672686515e-08, -4.60255583328996e-09, -2.8140172440362e-09, 1.15992321848839e-08, 1.55872817287606e-08, 4.64561534001302e-10, -9.36199917985853e-10, -3.30000706958992e-10, -1.57148994844309e-09, 6.47763140550062e-09, 4.64561534001302e-10, 1.75677385239271e-09, -5.22808409550424e-10, -1.84272727373226e-10, 3.16743399688553e-09, -1.30560672686515e-08, -9.36199917985853e-10, -5.22808409550424e-10, 4.60243376260227e-09, 3.71521422032048e-10, 1.11659687239979e-09, -4.60255583328996e-09, -3.30000706958992e-10, -1.84272727373226e-10, 3.71521422032048e-10, 6.55629183612458e-09, 1.8754261763856e-08, -7.73031094264582e-08, -5.54347406681391e-09, -3.09575799861647e-09, 6.23962311533508e-09, 2.19960982426364e-09, 1.7371432908383e-08, -7.16039279072896e-08, -5.13471720318283e-09, -2.86749094167462e-09, 5.77953554784623e-09, 2.03741514625023e-09, 0.000204507192785026, 3.96218053641124e-05, 1.0638090174294e-05, 1.61065860410035e-06, 6.08076132387482e-06, -4.62878478097471e-06, 3.96218053641124e-05, 0.00234308748966294, 0.000470020596846252, 7.11625828239816e-05, 0.000268663608247443, -0.000204511934881824, 1.0638090174294e-05, 0.000470020596846252, 0.00347589952822904, 1.91064920134712e-05, 7.21338005448661e-05, -5.49096706033319e-05, 1.61065860410035e-06, 7.11625828239816e-05, 1.91064920134712e-05, 0.000162208803157109, 1.0921332417337e-05, -8.31351204282455e-06, 6.08076132387482e-06, 0.000268663608247443, 7.21338005448661e-05, 1.0921332417337e-05, 0.000426405075762334, -3.13863780413286e-05, -4.62878478097471e-06, -0.000204511934881824, -5.49096706033319e-05, -8.31351204282455e-06, -3.13863780413286e-05, 0.000484340050623577, -6.40371054829753e-05, -0.00302315031152417, -0.000759618231467465, -0.000115014225811381, -0.000434207463850975, 0.000330524580872117, 6.59305846579617e-06, 0.000291302007193957, 7.82122829802096e-05, 1.18414170438043e-05, 4.47058211420251e-05, -3.40310103200913e-05, 0.000595627591790756, -1.98350763981961e-11, 3.91331324983701e-11, 3.09154657169436e-11, -1.85910286297497e-10, 4.14389647596103e-10, -1.98350763981961e-11, 0.00101876178563553, -8.68173176578335e-12, -6.85862922445574e-12, 4.12444804871737e-11, -9.19329430290605e-11, 3.91331324983701e-11, -8.68173176578335e-12, 0.00286690437068185, 1.35315878510914e-11, -8.13722218946655e-11, 1.81376779914699e-10, 3.09154657169436e-11, -6.85862922445574e-12, 1.35315878510914e-11, 0.000719564739496544, -6.42846544225695e-11, 1.43288999589208e-10, -1.85910286297497e-10, 4.12444804871737e-11, -8.13722218946655e-11, -6.42846544225695e-11, 0.00125167506309381, -8.61669211676963e-10, 4.14389647596103e-10, -9.19329430290605e-11, 1.81376779914699e-10, 1.43288999589208e-10, -8.61669211676963e-10, 0.000818895666242797, 6.81933854003447e-11, -1.51287890093159e-11, 2.98479919166178e-11, 2.35801376254757e-11, -1.41799223404848e-10, 3.16067141209464e-10, -1.3300845938969e-11, 2.95082481940965e-12, -5.82172407070231e-12, -4.59920204134642e-12, 2.76574001331284e-11, -6.16476633196611e-11, 0.000382188647098703, 9.20133193457273e-05, 0.000254400144161898, 0.000219767233912923, 0.000118171478661359, -0.000102338231280768, 9.20133193457273e-05, 0.000511500084436223, 8.04048954642997e-05, 8.45954491926936e-05, 9.68651898501585e-05, 0.000123516784705527, 0.000254400144161898, 8.04048954642997e-05, 0.00188017700353292, 0.00041533734802655, 0.000149139757186764, -0.0004294190307933, 0.000219767233912923, 8.45954491926936e-05, 0.00041533734802655, 0.000561433953395943, 0.000137923370189886, -0.00031102686876138, 0.000118171478661359, 9.68651898501585e-05, 0.000149139757186764, 0.000137923370189886, 0.000372837421428478, 3.41404996661138e-05, -0.000102338231280768, 0.000123516784705527, -0.0004294190307933, -0.00031102686876138, 3.41404996661138e-05, 0.00107380670893907, 0.000142016132344844, 0.000103321680113364, 0.000189064968920016, 0.000173700683259049, 0.000121189940378943, 1.38025891907582e-05, 8.87214762321567e-05, 0.000100424332953944, 7.18818694145038e-05, 7.79607181979821e-05, 9.57598660555519e-05, 0.000134421602409216, 0.000178283467503444, 0.000178278184073295, 0.000178276921940647, 0.000178282130042361, 0.000178279652493857, 0.000178277628716052, 0.000178278184073292, 0.000178311419270022, 0.000178318092984915, 0.000178281202824926, 0.000178298751865903, 0.000178313086737932, 0.000178276921940647, 0.000178318092984919, 0.000178336399506422, 0.000178280935159633, 0.000178304265381162, 0.000178323322590716, 0.000178282130042361, 0.000178281202824929, 0.000178280935159633, 0.000178283037822448, 0.000178281514238363, 0.000178281085048287, 0.000178279652493857, 0.000178298751865907, 0.000178304265381162, 0.000178281514238363, 0.000178294510846229, 0.000178301177895732, 0.000178277628716049, 0.000178313086737932, 0.000178323322590712, 0.000178281085048283, 0.000178301177895728, 0.000178320242015004, 0.000178277956737857, 0.000178310763286595, 0.000178320233724643, 0.000178281154613158, 0.000178299744961592, 0.000178314930421964, 0.000178277288880306, 0.00017831549387029, 0.000178326522704823, 0.00017828101297802, 0.000178302662438189, 0.000178320346723538, 0.000249255745722262, 1.40880624365891e-07, 1.9715500381946e-06, 1.44137714799125e-06, 3.07396479046597e-07, -4.51303962743701e-07, 1.40880624365891e-07, 0.00100342264674554, 1.42830751626548e-07, 1.0442104419827e-07, 2.22705038258351e-08, -3.26936348327063e-08, 1.9715500381946e-06, 1.42830751626548e-07, 0.00343307096443373, 1.46131897195423e-06, 3.11650344277689e-07, -4.57546769215339e-07, 1.44137714799125e-06, 1.0442104419827e-07, 1.46131897195423e-06, 0.000186512634321463, 2.27843126195592e-07, -3.34508047380045e-07, 3.07396479046597e-07, 2.22705038258351e-08, 3.11650344277689e-07, 2.27843126195592e-07, 0.000435506111955378, -7.13379201916996e-08, -4.51303962743701e-07, -3.26936348327063e-08, -4.57546769215339e-07, -3.34508047380045e-07, -7.13379201916996e-08, 0.00032656550202865, -1.45302778015036e-06, -1.05264256453213e-07, -1.473130071733e-06, -1.07698884906256e-06, -2.2968401122719e-07, 3.37212811064879e-07, 5.76881743374023e-07, 4.17935999858247e-08, 5.848641420848e-07, 4.27586436223693e-07, 9.11906872839524e-08, -1.33878629372092e-07, 0.000476168992138329, 1.95505236676857e-07, -1.96494067727059e-05, 1.6705981921647e-06, -5.90413303049736e-07, -2.73361238952233e-05, 1.95505236676857e-07, 0.00126654506228381, 5.61397091835593e-06, 6.97193737200785e-07, 1.22325348208586e-06, 7.37514675118629e-06, -1.96494067727059e-05, 5.61397091835593e-06, 0.00295317232758473, -4.61556787708425e-06, 1.1009786747453e-05, 0.00019559360022598, 1.6705981921647e-06, 6.97193737200785e-07, -4.61556787708425e-06, 0.000448459216604951, 4.84351901636551e-07, -6.67539108392332e-06, -5.90413303049736e-07, 1.22325348208586e-06, 1.1009786747453e-05, 4.84351901636551e-07, 0.000700663822569031, 1.47952436041175e-05, -2.73361238952233e-05, 7.37514675118629e-06, 0.00019559360022598, -6.67539108392332e-06, 1.47952436041175e-05, 0.00170799025564566, -1.31961287402264e-05, 4.12788685931432e-06, 9.80254410011738e-05, -2.88857963325778e-06, 7.82563767859671e-06, 0.000134378719960182, -1.3412966566235e-05, 4.17740510953442e-06, 9.95206733654617e-05, -2.94673627831521e-06, 7.93229002180084e-06, 0.000136433836552945, 0.000421979198726787, 1.13502443441796e-07, 4.73534292340979e-05, 6.65643627620295e-06, 4.90204982843e-06, -2.02431411253556e-06, 1.13502443441796e-07, 0.000583822495446347, -4.37931355281077e-05, -3.15894819838565e-06, 1.98956308238779e-06, 7.8354283101314e-06, 4.73534292340979e-05, -4.37931355281077e-05, 0.00436803302215065, 8.874997682797e-05, 3.7633586527917e-05, -7.32476741814054e-05, 6.65643627620295e-06, -3.15894819838565e-06, 8.874997682797e-05, 0.000409007711222281, 5.99510303218647e-06, -6.69934497095283e-06, 4.90204982843e-06, 1.98956308238779e-06, 3.7633586527917e-05, 5.99510303218647e-06, 0.000788317036838579, -1.71343463960651e-08, -2.02431411253556e-06, 7.8354283101314e-06, -7.32476741814054e-05, -6.69934497095283e-06, -1.71343463960651e-08, 0.0015250353968028, -2.1029179037886e-06, 8.30095299928014e-06, -7.70150021644302e-05, -7.04191064868456e-06, 4.39369919681448e-08, 1.06712685958719e-05, -3.47654986650815e-06, 8.89687070067821e-06, -9.54645533167561e-05, -9.27926214133528e-06, -1.2690706909683e-06, 1.20464648574159e-05, 0.000249756437369473, -8.33416335239631e-06, -3.44846565495686e-05, 1.58719291516668e-05, -1.86246542184531e-05, -1.56169034648021e-05, -8.33416335239631e-06, 0.00067735104886479, 0.000106509506671276, -2.79267269894539e-05, 7.41822929238144e-05, 6.09868079386546e-05, -3.44846565495686e-05, 0.000106509506671276, 0.00347343098442299, -7.83200055332438e-05, 0.000166466175699259, 0.000137868705430516, 1.58719291516668e-05, -2.79267269894539e-05, -7.83200055332438e-05, 0.000247760262522392, -4.81381140309172e-05, -3.98839091053278e-05, -1.86246542184531e-05, 7.41822929238144e-05, 0.000166466175699259, -4.81381140309172e-05, 0.000673005297244339, 9.23529330054558e-05, -1.56169034648021e-05, 6.09868079386546e-05, 0.000137868705430516, -3.98839091053278e-05, 9.23529330054558e-05, 0.00120726744934011, 1.62010213605479e-05, 1.17498258067481e-05, -1.19548487142989e-05, 1.5072691198294e-05, 3.11897863126704e-06, 1.34860040425797e-06, 1.35143196403646e-05, 1.10354442924136e-05, -7.53743234578001e-06, 1.21771407382868e-05, 4.32781586171102e-06, 2.58765789546014e-06, 5.84723353744217e-07, 5.66806597235321e-08, 5.45331376396812e-07, 2.84740219364165e-07, 2.16192206508e-07, 1.7487190102632e-07, 5.66806597235322e-08, 9.39636853520967e-07, -3.06560512281921e-07, 3.50208990017659e-08, 1.24202054663647e-07, 1.78413240768835e-07, 5.45331376396812e-07, -3.06560512281921e-07, 3.93454533297325e-06, 6.12070253157238e-07, 3.36985293286573e-07, 1.70220888475508e-07, 2.84740219364165e-07, 3.5020899001766e-08, 6.12070253157238e-07, 6.2259506502226e-07, 2.23391714417547e-07, 1.74595492236862e-07, 2.16192206508e-07, 1.24202054663646e-07, 3.36985293286573e-07, 2.23391714417547e-07, 6.91087192409985e-07, 1.75730311876578e-07, 1.7487190102632e-07, 1.78413240768835e-07, 1.70220888475508e-07, 1.74595492236862e-07, 1.75730311876578e-07, 8.17309705480943e-07, 3.62133562176226e-06, -2.13900739036425e-06, 1.04681674151376e-05, 4.03614796482439e-06, 2.30523689546651e-06, 1.28818395167377e-06, 3.20419085590143e-07, -1.23422694318489e-08, 7.57219890809184e-07, 3.46473982779527e-07, 2.39165398790199e-07, 1.73982425325082e-07, 0.000815425697065525, 0.000322983302059327, 0.000355803024467498, 0.000271459055634256, 0.000304269733382108, 0.00027499145557414, 0.000322983302059327, 0.00977568015145744, 0.0099610360454617, 0.00655251076072851, 0.00787846287951198, 0.00669526284240114, 0.000355803024467498, 0.0099610360454617, 0.017934130512115, 0.00755478832393643, 0.00908708912978019, 0.00771975591706234, 0.000271459055634256, 0.00655251076072851, 0.00755478832393643, 0.00636790267383328, 0.00598101961309056, 0.00508689343582039, 0.000304269733382108, 0.00787846287951198, 0.00908708912978019, 0.00598101961309056, 0.0085694021122118, 0.00611110457710638, 0.00027499145557414, 0.00669526284240114, 0.00771975591706234, 0.00508689343582039, 0.00611110457710638, 0.00659351995538288, 0.000267097385890687, 0.0063762465394884, 0.00735109333332331, 0.00484581768852353, 0.00582039621050936, 0.00495074086866018, 4.46556985217172e-05, -0.00261310530646169, -0.00303720863701038, -0.00194729814154248, -0.00237128478695276, -0.00199294456741381 ), dim = c(6L, 8L, 17L), dimnames = list(c(\"ALL\", \"Ast\", \"End\", \"Exc\", \"Inh\", \"Mic\"), c(\"ALL\", \"Ast\", \"End\", \"Exc\", \"Inh\", \"Mic\", \"OPC\", \"Oli\"), c(\"mash::mash::var1\", \"mash::mash::var2\", \"mash::mash::var3\", \"mash::mash::var4\", \"mash::mash::var5\", \"mash::mash::var6\", \"mash::mash::var7\", \"mash::mash::var8\", \"mash::mash::var9\", \"mash::mash::var10\", \"mash::mash::var11\", \"mash::mash::var12\", \"mash::mash::var13\", \"mash::mash::var14\", \"mash::mash::var15\", \"mash::mash::var16\", \"mash::mash::var17\"))) ..."]},"tests/fixtures/mash_posterior/fine_mapping.rds":{"kind":"rds","lines":["Object: data.frame [17 x 3]"," variants cs_order pip"," 1 mash::mash::var1 1 0.60"," 2 mash::mash::var2 1 0.40"," 3 mash::mash::var3 0 0.02"]},"tests/fixtures/mash/expected/mash_input.qss.rds":{"kind":"rds","lines":["Object: list [length 10]"," Components: strong.b, strong.s, random.b, random.s, null.b, null.s, random.z, null.z, ...","$strong.b: matrix/array [2 x 2]"," Mic_De_Jager_eQTL"," protocol_example::mash::chr22:15528675:A:G_region1.qss 3.0964631"," protocol_example::mash::chr22:15528699:A:G_region1.qss 0.3039547"," Ast_De_Jager_eQTL"," protocol_example::mash::chr22:15528675:A:G_region1.qss 0.2011453"," protocol_example::mash::chr22:15528699:A:G_region1.qss 4.5483141","","$strong.s: matrix/array [2 x 2]"," Mic_De_Jager_eQTL"," protocol_example::mash::chr22:15528675:A:G_region1.qss 1"," protocol_example::mash::chr22:15528699:A:G_region1.qss 1"," Ast_De_Jager_eQTL"," protocol_example::mash::chr22:15528675:A:G_region1.qss 1"," protocol_example::mash::chr22:15528699:A:G_region1.qss 1","","$random.b: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," protocol_example::mash::chr22:15528319:A:G_region1.qss 0.69777934"," protocol_example::mash::chr22:15529124:A:G_region1.qss 1.32852955"," protocol_example::mash::chr22:15528227:A:G_region1.qss -0.05627064"," Ast_De_Jager_eQTL"," protocol_example::mash::chr22:15528319:A:G_region1.qss -0.1991450"," protocol_example::mash::chr22:15529124:A:G_region1.qss -0.2385934"," protocol_example::mash::chr22:15528227:A:G_region1.qss 0.9808774","","$random.s: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," protocol_example::mash::chr22:15528319:A:G_region1.qss 1"," protocol_example::mash::chr22:15529124:A:G_region1.qss 1"," protocol_example::mash::chr22:15528227:A:G_region1.qss 1"," Ast_De_Jager_eQTL"," protocol_example::mash::chr22:15528319:A:G_region1.qss 1"," protocol_example::mash::chr22:15529124:A:G_region1.qss 1"," protocol_example::mash::chr22:15528227:A:G_region1.qss 1","","$null.b: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," protocol_example::mash::chr22:15528612:A:G_region1.qss 1.66040624"," protocol_example::mash::chr22:15528787:A:G_region1.qss -0.01514105"," protocol_example::mash::chr22:15529068:A:G_region1.qss 1.63336444"," Ast_De_Jager_eQTL"," protocol_example::mash::chr22:15528612:A:G_region1.qss -1.0569069"," protocol_example::mash::chr22:15528787:A:G_region1.qss -0.9860239"," protocol_example::mash::chr22:15529068:A:G_region1.qss 0.1641178","","$null.s: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," protocol_example::mash::chr22:15528612:A:G_region1.qss 1"," protocol_example::mash::chr22:15528787:A:G_region1.qss 1"," protocol_example::mash::chr22:15529068:A:G_region1.qss 1"," Ast_De_Jager_eQTL"," protocol_example::mash::chr22:15528612:A:G_region1.qss 1"," protocol_example::mash::chr22:15528787:A:G_region1.qss 1"," protocol_example::mash::chr22:15529068:A:G_region1.qss 1"]},"tests/fixtures/mash/expected/mash_input.fmr.rds":{"kind":"rds","lines":["Object: list [length 10]"," Components: strong.b, strong.s, random.b, random.s, null.b, null.s, random.z, null.z, ...","$strong.b: matrix/array [1 x 2]"," Mic_De_Jager_eQTL Ast_De_Jager_eQTL"," [1,] 2.70564 0.5429115","","$strong.s: matrix/array [1 x 2]"," Mic_De_Jager_eQTL Ast_De_Jager_eQTL"," [1,] 1 1","","$random.b: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," chr22:15528319:A:G_protocol_example.QtlFineMappingResult 0.69777934"," chr22:15529124:A:G_protocol_example.QtlFineMappingResult 1.32852955"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult -0.05627064"," Ast_De_Jager_eQTL"," chr22:15528319:A:G_protocol_example.QtlFineMappingResult -0.1991450"," chr22:15529124:A:G_protocol_example.QtlFineMappingResult -0.2385934"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult 0.9808774","","$random.s: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," chr22:15528319:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15529124:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult 1"," Ast_De_Jager_eQTL"," chr22:15528319:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15529124:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult 1","","$null.b: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," chr22:15528612:A:G_protocol_example.QtlFineMappingResult 1.66040624"," chr22:15528787:A:G_protocol_example.QtlFineMappingResult -0.01514105"," chr22:15529068:A:G_protocol_example.QtlFineMappingResult 1.63336444"," Ast_De_Jager_eQTL"," chr22:15528612:A:G_protocol_example.QtlFineMappingResult -1.0569069"," chr22:15528787:A:G_protocol_example.QtlFineMappingResult -0.9860239"," chr22:15529068:A:G_protocol_example.QtlFineMappingResult 0.1641178","","$null.s: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," chr22:15528612:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528787:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15529068:A:G_protocol_example.QtlFineMappingResult 1"," Ast_De_Jager_eQTL"," chr22:15528612:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528787:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15529068:A:G_protocol_example.QtlFineMappingResult 1"]},"tests/fixtures/mash/expected/mash_input.indep.rds":{"kind":"rds","lines":["Object: list [length 10]"," Components: strong.b, strong.s, random.b, random.s, null.b, null.s, random.z, null.z, ...","$strong.b: matrix/array [1 x 2]"," Mic_De_Jager_eQTL Ast_De_Jager_eQTL"," [1,] 2.70564 0.5429115","","$strong.s: matrix/array [1 x 2]"," Mic_De_Jager_eQTL Ast_De_Jager_eQTL"," [1,] 1 1","","$random.b: matrix/array [10 x 2]"," Mic_De_Jager_eQTL"," chr22:15528791:A:G_protocol_example.QtlFineMappingResult 0.8741938"," chr22:15528516:A:G_protocol_example.QtlFineMappingResult -2.8592052"," chr22:15528699:A:G_protocol_example.QtlFineMappingResult 0.3039547"," Ast_De_Jager_eQTL"," chr22:15528791:A:G_protocol_example.QtlFineMappingResult -0.0510958"," chr22:15528516:A:G_protocol_example.QtlFineMappingResult -1.2528124"," chr22:15528699:A:G_protocol_example.QtlFineMappingResult 4.5483141","","$random.s: matrix/array [10 x 2]"," Mic_De_Jager_eQTL"," chr22:15528791:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528516:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528699:A:G_protocol_example.QtlFineMappingResult 1"," Ast_De_Jager_eQTL"," chr22:15528791:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528516:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528699:A:G_protocol_example.QtlFineMappingResult 1","","$null.b: matrix/array [9 x 2]"," Mic_De_Jager_eQTL"," chr22:15528467:A:G_protocol_example.QtlFineMappingResult 0.57965162"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult -0.05627064"," chr22:15528746:A:G_protocol_example.QtlFineMappingResult 1.10137261"," Ast_De_Jager_eQTL"," chr22:15528467:A:G_protocol_example.QtlFineMappingResult 1.3747398"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult 0.9808774"," chr22:15528746:A:G_protocol_example.QtlFineMappingResult 0.6216373","","$null.s: matrix/array [9 x 2]"," Mic_De_Jager_eQTL"," chr22:15528467:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528746:A:G_protocol_example.QtlFineMappingResult 1"," Ast_De_Jager_eQTL"," chr22:15528467:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528746:A:G_protocol_example.QtlFineMappingResult 1"]},"tests/fixtures/mash/expected/mixture_prior.EE.prior.rds":{"kind":"rds","lines":["Object: list [length 3]"," Components: U, w, loglik","$U: list [length 32]"," Components: identity, ALL, Ast, End, Exc, Inh, Mic, OPC, ...","$w: numeric [length 33]"," Values: c(null = 0.350889466152308, identity = 0, ALL = 0, Ast = 0, End = 0.0626903097191792, Exc = 0) ...","$loglik: NULL [length 0]"]},"tests/fixtures/mash/expected/vhat.identity.EE.rds":{"kind":"rds","lines":["Object: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 1 0 0 0 0 0"," [2,] 0 1 0 0 0 0"," [3,] 0 0 1 0 0 0"]},"tests/fixtures/mash/expected/vhat.simple.EE.rds":{"kind":"rds","lines":["Object: matrix/array [8 x 8]"," ALL Ast End Exc Inh Mic"," ALL 1.00000000 0.01420407 -0.06297940 0.65424529 0.01352651 0.2149795"," Ast 0.01420407 1.00000000 0.05708375 0.01527867 0.19794257 -0.1509936"," End -0.06297940 0.05708375 1.00000000 -0.21535872 -0.02215867 -0.3384365"]},"tests/fixtures/mash/expected/vhat.corshrink.EE.rds":{"kind":"rds","lines":["Object: matrix/array [8 x 8]"," ALL Ast End Exc Inh"," ALL 1.0000000000 0.000987488 0.0005125989 6.504117e-01 0.0009814652"," Ast 0.0009874880 1.000000000 0.0014810321 9.971329e-04 0.0078452162"," End 0.0005125989 0.001481032 1.0000000000 9.332334e-05 0.0007185897"," Mic"," ALL 0.0100225824"," Ast 0.0002419493"," End -0.0004634544"]},"tests/fixtures/mash/expected/vhat.simple_specific.EE.rds":{"kind":"rds","lines":["Object: matrix/array [8 x 8]"," ALL Ast End Exc Inh Mic"," ALL 1.000000000 0.009577799 -0.04626552 0.4573655 0.009267642 0.1618731"," Ast 0.009577799 1.000000000 0.04184216 0.0106574 0.135321006 -0.1134433"," End -0.046265520 0.041842160 1.00000000 -0.1636567 -0.016503484 -0.2770151"]},"tests/fixtures/mash/expected/prior.cov_ed.EE.rds":{"kind":"rds","lines":["Object: list [length 3]"," Components: U, w, loglik","$U: list [length 34]"," Components: identity, ALL, Ast, End, Exc, Inh, Mic, OPC, ...","$w: numeric [length 35]"," Values: c(null = 0.350888658143542, identity = 0, ALL = 0, Ast = 0, End = 0.0581579432131964, Exc = 0) ...","$loglik: NULL [length 0]"]},"tests/fixtures/mash/expected/cov.canonical.EE.rds":{"kind":"rds","lines":["Object: list [length 13]"," Components: identity, ALL, Ast, End, Exc, Inh, Mic, OPC, ...","$identity: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 1 0 0 0 0 0"," [2,] 0 1 0 0 0 0"," [3,] 0 0 1 0 0 0","","$ALL: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 1 0 0 0 0 0"," [2,] 0 0 0 0 0 0"," [3,] 0 0 0 0 0 0","","$Ast: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 0 0 0 0 0 0"," [2,] 0 1 0 0 0 0"," [3,] 0 0 0 0 0 0","","$End: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 0 0 0 0 0 0"," [2,] 0 0 0 0 0 0"," [3,] 0 0 1 0 0 0","","$Exc: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 0 0 0 0 0 0"," [2,] 0 0 0 0 0 0"," [3,] 0 0 0 0 0 0","","$Inh: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 0 0 0 0 0 0"," [2,] 0 0 0 0 0 0"," [3,] 0 0 0 0 0 0"]},"tests/fixtures/mash/expected/cov.pca.EE.rds":{"kind":"rds","lines":["Object: list [length 4]"," Components: PCA_1, PCA_2, PCA_3, tPCA","$PCA_1: matrix/array [8 x 8]"," ALL Ast End Exc Inh Mic"," ALL 0.006180290 0.008174521 0.008739213 -0.007784481 0.003495496 0.02409971"," Ast 0.008174521 0.010812242 0.011559147 -0.010296345 0.004623408 0.03187610"," End 0.008739213 0.011559147 0.012357649 -0.011007613 0.004942791 0.03407809","","$PCA_2: matrix/array [8 x 8]"," ALL Ast End Exc Inh Mic"," ALL 0.02563814 0.03520979 0.1427297 0.03855221 0.004478845 0.01598269"," Ast 0.03520979 0.04835487 0.1960158 0.05294513 0.006150959 0.02194960"," End 0.14272971 0.19601585 0.7945883 0.21462338 0.024934105 0.08897698","","$PCA_3: matrix/array [8 x 8]"," ALL Ast End Exc Inh Mic"," ALL 0.17897232 -0.020181322 -0.15323506 0.17052991 0.071118778 0.12859069"," Ast -0.02018132 0.002275691 0.01727913 -0.01922934 -0.008019513 -0.01450018"," End -0.15323506 0.017279130 0.13119896 -0.14600671 -0.060891483 -0.11009860","","$tPCA: matrix/array [8 x 8]"," ALL Ast End Exc Inh Mic"," ALL 0.021681724 0.005798827 0.01206837 0.020227268 0.0078675632 0.019209544"," Ast 0.005798827 0.010575083 0.03695715 0.005074851 0.0012659803 0.008948697"," End 0.012068372 0.036957148 0.14821781 0.020771536 -0.0002572156 0.012099821"]},"tests/fixtures/mash/expected/cov.flash.EE.rds":{"kind":"rds","lines":["Object: list [length 0]"]},"tests/fixtures/mash/expected/cov.flash_nonneg.EE.rds":{"kind":"rds","lines":["Object: list [length 0]"]},"tests/fixtures/phenotype_formatting/regions.txt":{"kind":"table","rows":[["chr22","10939387","30861524","region1"],["chr22","30861524","50783661","region2"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/tad_list.txt":{"kind":"table","rows":[["#chr","start","end","index"],["chr22","10700000","12700000","TAD_1"],["chr22","13000000","15000000","TAD_2"],["chr22","15200000","17200000","TAD_3"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/keep_samples.txt":{"kind":"table","rows":[["SAMPLE_002"],["SAMPLE_003"],["SAMPLE_004"],["SAMPLE_005"]],"shownColumns":1,"totalColumns":1,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/expected/protocol_example.chr22.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","10939387","10961337","ENSG00000283047","37.0768403309204","0.0","5.5832744229102","0.0"],["chr22","15528191","15529138","ENSG00000130538","0.0","1.08358035439567","8.91397741376836","4.08850454279024"],["chr22","15611758","15613095","ENSG00000231565","5.97808406328782","0.0","2.63711285656005","10.4666167292313"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_chrom_files.txt":{"kind":"table","rows":[["#id","#dir"],["22","protocol_example.genotype.chr22.bed.gz"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_chrom_files.region_list.txt":{"kind":"table","rows":[["#chr","start","end","ID","path"],["chr22","10939387","10961337","ENSG00000283047","protocol_example.genotype.chr22.bed.gz"],["chr22","15528191","15529138","ENSG00000130538","protocol_example.genotype.chr22.bed.gz"],["chr22","15611758","15613095","ENSG00000231565","protocol_example.genotype.chr22.bed.gz"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region/protocol_example.region1.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","10939387","10961337","ENSG00000283047","37.0768403309204","0.0","5.5832744229102","0.0"],["chr22","15528191","15529138","ENSG00000130538","0.0","1.08358035439567","8.91397741376836","4.08850454279024"],["chr22","15611758","15613095","ENSG00000231565","5.97808406328782","0.0","2.63711285656005","10.4666167292313"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region/protocol_example.region2.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","30693781","30907823","ENSG00000184792","23.2978326159215","20.9704714755826","8.35869341969442","16.066159402042"],["chr22","30902218","30902780","ENSG00000237977","0.0","0.0","8.86506705966064","7.69079135082964"],["chr22","30971004","30971148","ENSG00000276664","0.0","0.0","0.0","2.83932127114085"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_region_files.txt":{"kind":"table","rows":[["#id","dir"],["region1","protocol_example.region1.bed.gz"],["region2","protocol_example.region2.bed.gz"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/expected/protocol_example.tpm.sample_matched.gct.gz":{"kind":"table","rows":[["#1.2"],["300","6"],["gene_ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","4.46908614068004","3.6324384389436","0","0.926449274182614","8.44864560635242","16.3456237133014","4.07740959667351"]],"shownColumns":8,"totalColumns":8,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/expected/protocol_example.rnaseq.bed.bed.gz.tad_list.txt.2_pheno_per_region.region_list":{"kind":"table","rows":[["#chr","start","end","ID","path"],["chr22","15200000","17200000","TAD_3","protocol_example.rnaseq.bed.bed.gz"],["chr22","17500000","19500000","TAD_4","protocol_example.rnaseq.bed.bed.gz"],["chr22","20000000","22000000","TAD_5","protocol_example.rnaseq.bed.bed.gz"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/expected/protocol_example.chr22.gct":{"kind":"table","rows":[["ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000283047","37.0768403309204","0.0","5.5832744229102","0.0","11.7772567385319","0.0","0.0"],["ENSG00000130538","0.0","1.08358035439567","8.91397741376836","4.08850454279024","4.14014751640196","0.0","0.0"],["ENSG00000231565","5.97808406328782","0.0","2.63711285656005","10.4666167292313","17.4660449424069","9.70082378235877","5.58310234009874"]],"shownColumns":8,"totalColumns":61,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/protocol_example.protein.missing.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","NA","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.EBMF.imputed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","-0.0331401044676228","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.knn.imputed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","-0.703447297160565","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.mean.imputed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","0.0391333975132811","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.lod.imputed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","-2.19704153370897","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.soft.imputed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","-0.288590023075699","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.filtered.imputed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","-0.288696212799218","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/pseudobulk_preprocessing/protocol_example.snrnaseq.seurat_MIC.rds":{"kind":"rds","lines":["Object: Seurat [13326 x 498]","@assays: list [length 1]"," Components: RNA","@meta.data: data.frame [498 x 5]"," orig.ident nCount_RNA nFeature_RNA celltype"," AAACCCACAAATGGTA_SAMPLE_001 SeuratProject 3198 1762 MIC"," AAAGAACTCATGAGGG_SAMPLE_001 SeuratProject 664 537 MIC"," AAAGGGCCAAGACCTT_SAMPLE_001 SeuratProject 2532 1551 MIC"," sample"," AAACCCACAAATGGTA_SAMPLE_001 SAMPLE_001"," AAAGAACTCATGAGGG_SAMPLE_001 SAMPLE_001"," AAAGGGCCAAGACCTT_SAMPLE_001 SAMPLE_001","","@active.assay: character [length 1]"," Values: \"RNA\"","@active.ident: factor [length 498]"," Values: structure(c(AAACCCACAAATGGTA_SAMPLE_001 = 1L, AAAGAACTCATGAGGG_SAMPLE_001 = 1L, AAAGGGCCAAGACCTT_SAMPLE_001 = 1L, AAAGGTAAGGGTACAC_SAMPLE_001 = 1L, AAAGTGATCTTGTTAC_SAMPLE_001 = 1L, AAATGGATCCTTCAGC_SAMPLE_001 = 1L ), levels = \"SeuratProject\", class = \"factor\") ...","@graphs: list [length 0]","@neighbors: list [length 0]"]},"tests/fixtures/pseudobulk_preprocessing/counts_MIC.csv.gz":{"kind":"table","rows":[["","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000000001","299","172","139","269","742","166","696"],["ENSG00000000002","533","624","49","2","1911","1822","679"],["ENSG00000000003","266","1254","2","96","69","87","474"]],"shownColumns":8,"totalColumns":51,"truncatedColumns":true},"tests/fixtures/pseudobulk_preprocessing/atac_MIC_residuals.txt":{"kind":"table","rows":[["","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["chr1-1000-1500","10.5316181036712","10.0782299856604","9.69847909370219","10.0321840665649","11.3624460645551","9.45339725517175","12.0088417718896"],["chr2-3000-3500","9.94704712753556","10.5923588918617","8.97464386590436","4.12683911798198","12.9509486373231","12.0693603093802","11.5287773654627"],["chr3-5000-5500","9.78294652491996","10.7874376477326","3.58479392625449","8.67490986347327","7.72750502355238","8.37133122984549","9.73624986316538"]],"shownColumns":8,"totalColumns":51,"truncatedColumns":true},"tests/fixtures/pseudobulk_preprocessing/expected/expected_counts_MIC.remapped.csv.gz":{"kind":"table","rows":[["","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000000001","299","172","139","269","742","166","696"],["ENSG00000000002","533","624","49","2","1911","1822","679"],["ENSG00000000003","266","1254","2","96","69","87","474"]],"shownColumns":8,"totalColumns":51,"truncatedColumns":true},"tests/fixtures/pseudobulk_preprocessing/expected/expected_MIC_residuals_qn.txt":{"kind":"table","rows":[["","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000000001","0.273701889612983","-0.0245772610640276","-0.273701889612983","-0.0737912738082727","0.786845099455005","-0.430727299295457","1.41570209380051"],["ENSG00000000002","-0.541395085129088","-0.0245772610640276","-1.00743560128731","-1.75986102793353","1.5647264713618","0.928899491647271","0.599229868099345"],["ENSG00000000003","0.377391943828554","0.721522283982343","-2.06191650080946","-0.430727299295457","-0.928899491647271","-0.599229868099345","0.273701889612983"]],"shownColumns":8,"totalColumns":51,"truncatedColumns":true},"tests/fixtures/qtl_association_postprocessing/protocol_example.cis_qtl.pairs.tsv.gz":{"kind":"table","rows":[["chrom","pos","molecular_trait_id","variant_id","tss_distance","tes_distance","af","ma_samples"],["22","10685239","ENSG00000283047","chr22:10685239_C_T","-254149","-276098","0.058333334","7"],["22","10761227","ENSG00000283047","chr22:10761227_G_A","-178161","-200110","0.15","18"],["22","11285239","ENSG00000283047","chr22:11285239_C_T","345851","323902","0.083333336","10"]],"shownColumns":8,"totalColumns":15,"truncatedColumns":true},"tests/fixtures/qtl_association_postprocessing/protocol_example.cis_qtl.regional.tsv.gz":{"kind":"table","rows":[["chrom","pos","n_variants","beta_shape1","beta_shape2","true_df","p_true_df","variant_id"],["22","11797697","6","0.9714302","5.6756625","29.047987","0.03418384894248458","chr22:11797697_C_T"],["22","15838003","51","1.0111347","30.198004","28.527073","0.01017646989997189","chr22:15838003_CTTTCTTTTTCTTT_ATTTCTTTTTCTTT"],["22","15838010","49","0.9969245","25.608551","27.582878","0.04197258326039418","chr22:15838010_TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC_TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC"]],"shownColumns":8,"totalColumns":21,"truncatedColumns":true},"tests/fixtures/qtl_association_postprocessing/protocol_example.maf_0.01_window_1000000_cis_n_variants_stats.tsv.gz":{"kind":"table","rows":[["chrom","molecular_trait_object_id","n_variants","n_variants_filtered"],["chr22","ENSG00000099968","114","114"],["chr22","ENSG00000130538","43","43"],["chr22","ENSG00000215270","51","51"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/qtl_association_postprocessing/expected/qap.cis_regional.fdr.tsv.gz":{"kind":"table","rows":[["chrom","pos","n_variants","beta_shape1","beta_shape2","true_df","p_true_df","variant_id"],["22","11797697","6","0.9714302","5.6756625","29.047987","0.03418384894248458","chr22:11797697_C_T"],["22","15838003","51","1.0111347","30.198004","28.527073","0.01017646989997189","chr22:15838003_CTTTCTTTTTCTTT_ATTTCTTTTTCTTT"],["22","15838010","49","0.9969245","25.608551","27.582878","0.04197258326039418","chr22:15838010_TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC_TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC"]],"shownColumns":8,"totalColumns":31,"truncatedColumns":true},"tests/fixtures/qtl_association_postprocessing/expected/qap.summary.tsv":{"kind":"table","rows":[["method","significant_events","significant_qtl"],["permutation","0","0"],["bonferroni_original","0","0"],["bonferroni_filtered","0","0"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/reference_data_preparation/hgnc_chr22.tsv.gz":{"kind":"table","rows":[["Approved symbol","Previous symbols","Alias symbols","Chromosome","Ensembl gene ID","Ensembl ID(supplied by Ensembl)"],["A4GALT","P1","A14GALT, Gb3S, P(k)","22q13.2","ENSG00000128274","ENSG00000128274"],["ABCD1P4","","","22q11.1","ENSG00000225293","ENSG00000225293"],["ABHD17AP4","FAM108A5, FAM108A5P","","22q11.21","ENSG00000229107","ENSG00000229107"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/reference_data_preparation/mini.gff3":{"kind":"table","rows":[["##gff-version 3"],["22","havana","gene","1000","5000",".","+","."],["22","havana","mRNA","1000","5000",".","+","."],["22","havana","exon","1000","2000",".","+","."]],"shownColumns":8,"totalColumns":9,"truncatedColumns":true},"tests/fixtures/reference_data_preparation/ERCC92.gtf":{"kind":"table","rows":[["ERCC-00002","ERCC","exon","1","1061","0.000000","+","."],["ERCC-00003","ERCC","exon","1","1023","0.000000","+","."],["ERCC-00004","ERCC","exon","1","523","0.000000","+","."],["ERCC-00009","ERCC","exon","1","984","0.000000","+","."]],"shownColumns":8,"totalColumns":9,"truncatedColumns":true},"tests/fixtures/reference_data_preparation/expected/hg_reference_1.filtered.fasta":{"kind":"table","rows":[[">chr22","normal"],["ACGTACGTACGT"],[">chr1_KI270706v1_random","rnd"],["TTTTTTTT"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/reference_data_preparation/expected/hg_gtf_1.reformatted.gtf":{"kind":"table","rows":[["22","havana","gene","15749156","15750825",".","-","."],["22","havana","transcript","15749156","15750825",".","-","."],["22","havana","exon","15750372","15750825",".","-","."],["22","havana","exon","15749156","15749798",".","-","."]],"shownColumns":8,"totalColumns":9,"truncatedColumns":true},"tests/fixtures/reference_data_preparation/expected/faidx.test_contigs.fa.fai":{"kind":"table","rows":[["chr22","12","14","12","13"],["chr1_KI270706v1_random","8","55","8","9"],["chr19_KI270938v1_alt","8","96","8","9"],["HLA-A*01:01:01:01","8","128","8","9"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/reference_data_preparation/expected/mini.gtf":{"kind":"table","rows":[["##gff-version 2"],["##source-version rtracklayer 1.70.1"],["##date 2026-08-13"],["22","havana","transcript","1000","5000",".","+","."]],"shownColumns":8,"totalColumns":9,"truncatedColumns":true},"tests/fixtures/reference_data_preparation/expected/hg38.chr22_SE_strict.ioe":{"kind":"table","rows":[["seqname","gene_id","event_id","alternative_transcripts","total_transcripts"],["chr22","ENSG00000075234","ENSG00000075234;SE:chr22:46268591-46269142:46269289-46272335:+","ENST00000417709","ENST00000381031,ENST00000417709,ENST00000421359"],["chr22","ENSG00000075234","ENSG00000075234;SE:chr22:46281718-46281971:46282151-46283973:+","ENST00000422713","ENST00000381031,ENST00000422713"],["chr22","ENSG00000075234","ENSG00000075234;SE:chr22:46289899-46292203:46292328-46292791:+","ENST00000451998","ENST00000381031,ENST00000451998"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/reference_data_preparation/expected/chr22.SUPPA_annotation.rds":{"kind":"rds","lines":["Object: list [length 7]"," Components: Alternative 3' splice site, Alternative 5' splice site, Alternative first exon, Alternative last exon, Mutually exclusive exon, Retained intron, Skipped exon","$Alternative 3' splice site: data.frame [66 x 7]"," Chromosome Strand Gene Constitutive exon 1 end"," 2 22 - ENSG00000099899 20112911"," 3 22 - ENSG00000099899 20113686"," 1 22 - ENSG00000099899 20114761"," Alternative exon 1 start Alternative exon 2 start"," 2 20112794 20112816"," 3 20113507 20113561"," 1 20114681 20114685","","$Alternative 5' splice site: data.frame [22 x 7]"," Chromosome Strand Gene Alternative exon 1 end"," 78 22 + ENSG00000099968 17638886"," 79 22 + ENSG00000284294 18939757"," 67 22 - ENSG00000099899 20112911"," Alternative exon 2 end Constitutive exon 2 start"," 78 17638700 17655662"," 79 18939749 18946791"," 67 20112956 20112794","","$Alternative first exon: data.frame [109 x 9]"," Chromosome Strand Gene Alternative exon 1 start"," 113 22 + ENSG00000100181 16601887"," 114 22 + ENSG00000100181 16601887"," 115 22 + ENSG00000099968 17628855"," Alternative exon 1 end Alternative exon 2 start"," 113 16602215 16637020"," 114 16602215 16637040"," 115 17628906 17628916","","$Alternative last exon: data.frame [64 x 9]"," Chromosome Strand Gene Constitutive exon 1 end"," 214 22 + ENSG00000100181 16638740"," 215 22 + ENSG00000100181 16638740"," 213 22 + ENSG00000100181 16638740"," Alternative exon 1 start Alternative exon 1 end"," 214 16639298 16640737"," 215 16639298 16640737"," 213 16648527 16653809","","$Mutually exclusive exon: data.frame [18 x 10]"," Chromosome Strand Gene Constitutive exon 1 end"," 269 22 + ENSG00000099968 17655832"," 267 22 + ENSG00000099968 17683321"," 270 22 + ENSG00000099968 17683321"," Alternative exon 1 start Alternative exon 1 end"," 269 17683214 17683321"," 267 17688986 17689142"," 270 17688986 17689142","","$Retained intron: data.frame [13 x 8]"," Chromosome Strand Gene Constitutive exon 1 start"," 287 22 + ENSG00000099942 20949711"," 288 22 + ENSG00000133460 23882759"," 289 22 + ENSG00000133460 23882759"," Constitutive exon 1 end Constitutive exon 2 start"," 287 20949927 20953206"," 288 23882869 23883874"," 289 23882869 23883949"]},"tests/fixtures/rss_analysis/protocol_example.rss_mwe.gwas_meta.tsv":{"kind":"table","rows":[["study_id","path","column_mapping","n_case","n_control"],["AD_Bellenguez_2022","protocol_example.gwas_sumstats.chr22.tsv.gz","protocol_example.gwas_column_mapping.yml","111326","677663"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/rss_analysis/protocol_example.gwas_sumstats.chr22.tsv.gz":{"kind":"table","rows":[["#chrom","pos","variant_id","A1","A2","Var","raiss_ld_score","raiss_R2"],["22","49000033","22:49000033:G:A","A","G","-1","Inf","NA"],["22","49000054","22:49000054:G:T","T","G","-1","Inf","NA"],["22","49000336","22:49000336:G:A","A","G","-1","Inf","NA"]],"shownColumns":8,"totalColumns":19,"truncatedColumns":true},"tests/fixtures/rss_analysis/protocol_example.gwas_column_mapping.yml":{"kind":"table","rows":[["chrom:","chrom"],["pos:","pos"],["A1:","A1"],["A2:","A2"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/rss_ld_sketch/protocol_example.ld_blocks.bed":{"kind":"table","rows":[["#chr","start","end"],["chr22","16000000","20000000"],["chr22","30000000","34000000"],["chr22","44000000","48000000"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/rss_ld_sketch/protocol_example.genotype.chr22.vcf.gz":{"kind":"table","rows":[["##fileformat=VCFv4.2"],["##FILTER="],["##fileDate=20231023"],["##source=PLINKv1.90"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/sldsc_enrichment/target.tsv":{"kind":"table","rows":[["chr","pos"],["1","888659"],["1","2974852"],["1","3168280"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/sldsc_enrichment/reference.2.bim":{"kind":"table","rows":[["2","rs10865542","1.2160932","1081594","G","T"],["2","rs13015040","2.5067138","1861586","G","A"],["2","rs719876","4.0279336","2654789","G","A"],["2","rs934558","4.7502589","2871548","T","G"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/sldsc_enrichment/expected/sldsc_postprocess.rds":{"kind":"rds","lines":["Object: list [length 3]"," Components: per_trait, meta, params","$per_trait: list [length 3]"," Components: sumstats.parquet, sumstats2.parquet, sumstats3.parquet","$meta: list [length 3]"," Components: tauStar, enrichment, enrichstat","$params: list [length 7]"," Components: maf_cutoff, M_ref, target_categories, n_baseline, baseline_categories, trait_names, target_categories_orig"]},"tests/fixtures/sldsc_enrichment/expected/sldsc_meta_subset.rds":{"kind":"rds","lines":["Object: list [length 4]"," Components: tau_star_single, tau_star_joint, enrichment, enrichstat","$tau_star_single: list [length 1]"," Components: ANNOT_0","$tau_star_joint: list [length 1]"," Components: ANNOT_0","$enrichment: list [length 1]"," Components: ANNOT_0","$enrichstat: list [length 1]"," Components: ANNOT_0"]},"tests/fixtures/sldsc_enrichment/expected/sldsc_meta_subset.notebook.rds":{"kind":"rds","lines":["Object: list [length 4]"," Components: tau_star_single, tau_star_joint, enrichment, enrichstat","$tau_star_single: list [length 1]"," Components: ANNOT_0","$tau_star_joint: list [length 1]"," Components: ANNOT_0","$enrichment: list [length 1]"," Components: ANNOT_0","$enrichstat: list [length 1]"," Components: ANNOT_0"]},"tests/fixtures/snrnaseq_preprocessing/protocol_example.snrnaseq.seurat_ref_SE.rds":{"kind":"rds","lines":["Object: SummarizedExperiment [length 13326]","@colData: DFrame [1050 x 1]","@assays: SimpleAssays [13326 x 1050]","@NAMES: character [length 13326]"," Values: c(\"NOC2L\", \"KLHL17\", \"HES4\", \"ISG15\", \"AGRN\", \"C1orf159\") ...","@elementMetadata: DFrame [13326 x 0]","@metadata: list [length 0]"]},"tests/fixtures/snrnaseq_preprocessing/protocol_example.snrnaseq.id_mapping.csv":{"kind":"table","rows":[["libraryBatch","cellBarcode","individualID"],["200225-B10-A","AAACGCTCAGACGATG-1","R6249698"],["200225-B10-A","AAAGAACCAGTTTCGA-1","R7840275"],["200225-B10-A","AAATGGAGTATCGTGT-1","R7698313"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/splicing_calling/leafcutter/SAMPLE_001.junc.gz":{"kind":"table","rows":[["chr22","11869845","11873926","JUNC00000001","1","+","11869845","11873926"],["chr22","11873885","11876132","JUNC00000002","1","+","11873885","11876132"],["chr22","11876103","11876296","JUNC00000003","2","+","11876103","11876296"],["chr22","11876223","11882340","JUNC00000004","3","+","11876223","11882340"]],"shownColumns":8,"totalColumns":12,"truncatedColumns":true},"tests/fixtures/splicing_calling/leafcutter/SAMPLE_002.junc.gz":{"kind":"table","rows":[["chr22","11478670","11478844","JUNC00000001","1","-","11478670","11478844"],["chr22","11478790","11479030","JUNC00000002","2","-","11478790","11479030"],["chr22","11903069","11903829","JUNC00000003","1","+","11903069","11903829"],["chr22","12314778","12319531","JUNC00000004","23","-","12314778","12319531"]],"shownColumns":8,"totalColumns":12,"truncatedColumns":true},"tests/fixtures/splicing_calling/psichomics/expected_junctions.txt":{"kind":"table","rows":[["Junction ID","SAMPLE_001.","SAMPLE_002."],["chr22:11478699:11478784:-","0","1"],["chr22:11478905:11478991:-","0","1"],["chr22:11869898:11873841:+","1","0"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/splicing_normalization/raw_data.txt.gz":{"kind":"table","rows":[["#Chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","16671178","16671518","chr22:16671178:16671518:clu_27_-","0.6302521008403361","0.3793103448275862","1.0327868852459017","1.8372093023255813"],["chr22","16671588","16673600","chr22:16671588:16673600:clu_27_-","0.13253012048192772","0.504","0.1794871794871795","0.0410958904109589"],["chr22","16673752","16675123","chr22:16673752:16675123:clu_27_-","0.26153846153846155","0.4430379746835443","0.696969696969697","0.7721518987341772"]],"shownColumns":8,"totalColumns":24,"truncatedColumns":true},"tests/fixtures/splicing_normalization/psi_raw_data.tsv.gz":{"kind":"table","rows":[["ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["SE_22_+_42438332_42438832_42439332_42439832_ENSG00000000000","NA","0.3414","0.1858","NA","0.6358","0.1152","NA"],["SE_22_-_42440332_42440832_42441332_42441832_ENSG00000000001","0.7942","0.1614","0.2509","0.6147","0.9029","0.5694","0.4070"],["SE_22_+_42442332_42442832_42443332_42443832_ENSG00000000002","0.1065","0.1036","0.2354","0.6624","0.4348","0.3327","0.5770"]],"shownColumns":8,"totalColumns":21,"truncatedColumns":true},"tests/fixtures/splicing_normalization/expected.phen_chr22.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","42438332","42440491","chr22:42438332:42440491:clu_1_+","2.6","0.05785123966942149","1.3404255319148937","1.392156862745098"],["chr22","42440604","42445702","chr22:42440604:42445702:clu_1_+","0.36","0.17880794701986755","1.2461538461538462","0.0064516129032258064"],["chr22","42445816","42446163","chr22:42445816:42446163:clu_1_+","0.30097087378640774","0.30275229357798167","0.6062992125984252","0.2740740740740741"]],"shownColumns":8,"totalColumns":24,"truncatedColumns":true},"tests/fixtures/splicing_normalization/expected/expected.prepare_phenotype.ave":{"kind":"table","rows":[["chr22:42438332:42440491:clu_1_+","0.006289308176100629","2.6","0.7474529958081921"],["chr22:42440604:42445702:clu_1_+","0.0064516129032258064","1.2461538461538462","0.5161248157417131"],["chr22:42445816:42446163:clu_1_+","0.11578947368421053","2.085714285714286","0.48602444984606896"],["chr22:38991618:38992398:clu_2_-","0.006369426751592357","14.6","1.780681536897999"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/splicing_normalization/expected/expected.prepare_phenotype.phenotype_file_list.txt":{"kind":"table","rows":[["#chr","#dir"],["chr22","leafcutter_perind.counts.gz.qqnorm_chr22"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/twas/protocol_example.twas.gwas_meta.tsv":{"kind":"table","rows":[["study_id","chrom","file_path","sample_size"],["protocol_example_twas_chr22","22","tests/fixtures/twas/protocol_example.twas.gwas_sumstats.chr22.tsv.gz","200000"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/twas/protocol_example.twas.xqtl_meta.tsv":{"kind":"table","rows":[["#chr","start","end","region_id","TSS","original_data","contexts"],["chr22","10000000","19000000","ENSG00000130538","15528191","tests/fixtures/twas/protocol_example.twas.reshaped_toy.chr22_ENSG00000130538.univariate_twas_weights.rds","bulk_rnaseq"]],"shownColumns":7,"totalColumns":7,"truncatedColumns":false},"tests/fixtures/twas/expected/twas.chr22.rds":{"kind":"rds","lines":["Object: GRanges [length 1]","@seqnames: Rle [length 1]","@ranges: IRanges [length 1]","@strand: Rle [length 1]","@seqinfo: Seqinfo [length 1]","@elementMetadata: DFrame [1 x 14]","@elementType: character [length 1]"," Values: \"ANY\""]},"tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bim":{"kind":"table","rows":[["22","chr22:10414272:A:T","0","10414272","A","T"],["22","chr22:10416111:A:T","0","10416111","A","T"],["22","chr22:10416669:A:T","0","10416669","A","T"],["22","chr22:10420511:A:T","0","10420511","A","T"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/qtl_mini/protocol_example.genotype.chr22.fam":{"kind":"table","rows":[["SAMPLE_001","SAMPLE_001","0","0","0","-9"],["SAMPLE_002","SAMPLE_002","0","0","0","-9"],["SAMPLE_003","SAMPLE_003","0","0","0","-9"],["SAMPLE_004","SAMPLE_004","0","0","0","-9"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/qtl_mini/example_geneexpr.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","10939387","10961338","ENSG00000283047","360","128","203","105"],["chr22","15528191","15529139","ENSG00000130538","125","180","220","195"],["chr22","15611758","15613096","ENSG00000231565","205","173","188","227"]],"shownColumns":8,"totalColumns":53,"truncatedColumns":true},"tests/fixtures/qtl_mini/example_covariates.tsv":{"kind":"table","rows":[["ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","0","1","0","1"],["age","67.06","82.92","87.76","64.57","81.62","66.44","75.53"],["PC1","-0.7904","-0.1993","0.3059","2.1952","-0.0345","-0.4571","0.7942"]],"shownColumns":8,"totalColumns":50,"truncatedColumns":true},"tests/fixtures/qtl_mini/association_windows.bed":{"kind":"table","rows":[["#chr","start","end","ID"],["chr22","10439387","11461338","ENSG00000283047"],["chr22","15028191","16029139","ENSG00000130538"],["chr22","15111758","16113096","ENSG00000231565"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/tensorqtl/expected/cis_qtl.pairs.tsv.gz":{"kind":"table","rows":[["chrom","pos","molecular_trait_id","variant_id","tss_distance","tes_distance","af","ma_samples"],["22","10414272","ENSG00000283047","chr22:10414272:A:T","-525115","-547066","0.5","37"],["22","10416111","ENSG00000283047","chr22:10416111:A:T","-523276","-545227","0.82653064","16"],["22","10416669","ENSG00000283047","chr22:10416669:A:T","-522718","-544669","0.622449","26"]],"shownColumns":8,"totalColumns":14,"truncatedColumns":true},"tests/fixtures/tensorqtl/expected/cis_qtl.regional.tsv.gz":{"kind":"table","rows":[["chrom","pos","n_variants","beta_shape1","beta_shape2","true_df","p_true_df","variant_id"],["22","10456420","200","0.9921782","197.45865","41.613945","0.0017812020290065426","chr22:10456420:A:T"],["22","15966274","1795","1.0157346","1877.0605","42.30297","0.0009428488229498306","chr22:15966274:A:T"],["22","16138746","1795","1.0108896","1879.0338","42.30057","3.083581953564483e-05","chr22:16138746:A:T"]],"shownColumns":8,"totalColumns":21,"truncatedColumns":true},"tests/fixtures/mash/expected/mash_sumstats.region1.rds":{"kind":"rds","lines":["Object: QtlSumStats [length 5]","@ldSketch: NULL [length 0]","@genome: character [length 1]"," Values: \"GRCh38\"","@qcInfo: list [length 2]"," Components: role, entryAudit","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 2L","@elementType: character [length 1]"," Values: \"ANY\""]},"tests/fixtures/qtl_association_postprocessing/expected/qap.rds":{"kind":"rds","lines":["Object: QtlSumStats [length 19]","@ldSketch: NULL [length 0]","@genome: character [length 1]"," Values: \"hg38\"","@qcInfo: list [length 1]"," Components: associationPostprocess","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 10L","@elementType: character [length 1]"," Values: \"ANY\""]},"tests/fixtures/rss_analysis/expected/gwas_sumstats.rds":{"kind":"rds","lines":["Object: GwasSumStats [length 5]","@ldSketch: GenotypeHandle [length 1]","@genome: character [length 1]"," Values: \"GRCh38\"","@qcInfo: list [length 3]"," Components: timestamp, options, entryAudit","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 1L","@elementType: character [length 1]"," Values: \"ANY\""]},"tests/fixtures/rss_analysis/expected/gwas_finemap.rds":{"kind":"rds","lines":["Object: GwasFineMappingResult [length 5]","@ldSketch: GenotypeHandle [length 1]","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 1L","@elementType: character [length 1]"," Values: \"ANY\"","@elementMetadata: NULL [length 0]","@metadata: list [length 0]"]},"tests/fixtures/twas/expected/gwas_sumstats.chr22.rds":{"kind":"rds","lines":["Object: GwasSumStats [length 3]","@ldSketch: GenotypeHandle [length 1]","@genome: character [length 1]"," Values: \"GRCh38\"","@qcInfo: list [length 3]"," Components: timestamp, options, entryAudit","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 1L","@elementType: character [length 1]"," Values: \"ANY\""]},"tests/fixtures/mnm_regression/expected/univariate_bvsr.rds":{"kind":"rds","lines":["Object: QtlFineMappingResult [length 7]","@ldSketch: NULL [length 0]","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 2L","@elementType: character [length 1]"," Values: \"ANY\"","@elementMetadata: NULL [length 0]","@metadata: list [length 0]"]},"tests/fixtures/mnm_regression/expected/univariate_twas_weights.rds":{"kind":"rds","lines":["Object: TwasWeights [length 7]","@ldSketch: NULL [length 0]","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 20L","@elementType: character [length 1]"," Values: \"ANY\"","@elementMetadata: NULL [length 0]","@metadata: list [length 0]"]}}; +const BENCH={"twas_ctwas":{"seconds":311.3,"tests":1},"methylation_calling":{"seconds":250.9,"tests":2},"snRNAseq_preprocessing":{"seconds":221.1,"tests":3},"reference_data_preparation":{"seconds":195.6,"tests":13},"gsea":{"seconds":157.2,"tests":1},"mnm_postprocessing":{"seconds":152.9,"tests":7},"TensorQTL":{"seconds":147.6,"tests":3},"sldsc_enrichment":{"seconds":146.4,"tests":6},"mnm_regression":{"seconds":142.6,"tests":1},"rss_ld_sketch":{"seconds":113.2,"tests":6},"covariate_hidden_factor":{"seconds":113.2,"tests":7},"gene_annotation":{"seconds":99.1,"tests":5},"phenotype_imputation":{"seconds":95.9,"tests":10},"mash_fit":{"seconds":93.0,"tests":1},"phenotype_formatting":{"seconds":72.6,"tests":6},"rss_analysis":{"seconds":71.2,"tests":1},"PCA":{"seconds":67.8,"tests":5},"SuSiE_enloc":{"seconds":67.1,"tests":1},"colocboost":{"seconds":60.1,"tests":1},"mixture_prior":{"seconds":54.2,"tests":1},"qtl_association_postprocessing":{"seconds":28.6,"tests":1},"mash_preprocessing":{"seconds":24.9,"tests":1},"bulk_expression_QC":{"seconds":24.1,"tests":4},"apa_impute":{"seconds":23.5,"tests":1},"mash_posterior":{"seconds":22.7,"tests":1},"GWAS_QC":{"seconds":19.8,"tests":8},"intact":{"seconds":19.8,"tests":1},"eoo_enrichment":{"seconds":19.1,"tests":1},"gregor":{"seconds":18.7,"tests":2},"ems_training":{"seconds":14.8,"tests":3},"VCF_QC":{"seconds":12.4,"tests":5},"generalized_TADB":{"seconds":10.2,"tests":1},"covariate_formatting":{"seconds":9.9,"tests":2},"ld_prune_reference":{"seconds":7.4,"tests":2},"genotype_formatting":"23s on toy data (8 workflows)","splicing_normalization":"32s on toy data (4 workflows)","splicing_calling":"50s on toy data (5 workflows)","apa_calling":"22s on toy data (6 workflows)","RNA_calling":"1m 20s on toy data (16 workflows)","bulk_expression_normalization":"12s on toy data","pseudobulk_preprocessing":"30s on toy data (4 workflows)"},FIXTURES={"methylation_calling":{"dir":"tests/fixtures/methylation_calling","dirs":["tests/fixtures/methylation_calling","tests/fixtures/methylation_calling/expected"],"inputs":["tests/fixtures/methylation_calling/protocol_example.methylation.sample_sheet_int.csv"],"outputs":["tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sesame.beta.bed.gz","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sesame.M.bed.gz","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sesame.gene_id.annot.tsv","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sample_qcs.sesame.tsv"],"files":["tests/fixtures/methylation_calling/protocol_example.methylation.sample_sheet_int.csv","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sesame.beta.bed.gz","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sesame.M.bed.gz","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sesame.gene_id.annot.tsv","tests/fixtures/methylation_calling/expected/protocol_example.methylation.sample_sheet_int.sample_qcs.sesame.tsv"]},"GWAS_QC":{"dir":"tests/fixtures/gwas_qc","dirs":["tests/fixtures/gwas_qc","tests/fixtures/gwas_qc/expected"],"inputs":["tests/fixtures/gwas_qc/protocol_example.pheno.bed","tests/fixtures/gwas_qc/protocol_example.kin0"],"outputs":["tests/fixtures/gwas_qc/expected/king.kin0","tests/fixtures/gwas_qc/expected/king_2.related_id","tests/fixtures/gwas_qc/expected/king_split.unrelated.fam","tests/fixtures/gwas_qc/expected/king_split.related.fam","tests/fixtures/gwas_qc/expected/qc_no_prune.bim","tests/fixtures/gwas_qc/expected/qc_ld_prune.prune.in","tests/fixtures/gwas_qc/expected/qc_ld_prune.bim","tests/fixtures/gwas_qc/expected/sample_overlap.txt","tests/fixtures/gwas_qc/expected/king_workflow.unrelated.fam"],"files":["tests/fixtures/gwas_qc/protocol_example.pheno.bed","tests/fixtures/gwas_qc/protocol_example.kin0","tests/fixtures/gwas_qc/expected/king.kin0","tests/fixtures/gwas_qc/expected/king_2.related_id","tests/fixtures/gwas_qc/expected/king_split.unrelated.fam","tests/fixtures/gwas_qc/expected/king_split.related.fam","tests/fixtures/gwas_qc/expected/qc_no_prune.bim","tests/fixtures/gwas_qc/expected/qc_ld_prune.prune.in","tests/fixtures/gwas_qc/expected/qc_ld_prune.bim","tests/fixtures/gwas_qc/expected/sample_overlap.txt","tests/fixtures/gwas_qc/expected/king_workflow.unrelated.fam"]},"PCA":{"dir":"tests/fixtures/pca","dirs":["tests/fixtures/pca","tests/fixtures/pca/expected"],"inputs":["tests/fixtures/pca/protocol_example.pca_pheno.txt","tests/fixtures/pca/protocol_example.unrelated.prune.bed"],"outputs":["tests/fixtures/pca/expected/project_samples.rds","tests/fixtures/pca/expected/detect_outliers.maha.rds","tests/fixtures/pca/expected/detect_outliers.outliers.txt","tests/fixtures/pca/expected/pca_plink.eigenvec","tests/fixtures/pca/expected/flashpca.eigenvalues.tsv"],"files":["tests/fixtures/pca/protocol_example.pca_pheno.txt","tests/fixtures/pca/protocol_example.unrelated.prune.bed","tests/fixtures/pca/expected/project_samples.rds","tests/fixtures/pca/expected/detect_outliers.maha.rds","tests/fixtures/pca/expected/detect_outliers.outliers.txt","tests/fixtures/pca/expected/pca_plink.eigenvec","tests/fixtures/pca/expected/flashpca.eigenvalues.tsv"]},"RNA_calling":{"dir":"tests/fixtures/rna_calling","dirs":["tests/fixtures/rna_calling","tests/fixtures/rna_calling/expected"],"inputs":["tests/fixtures/rna_calling/protocol_example.rnaseq.fastq.list.txt","tests/fixtures/rna_calling/SAMPLE_001.rnaseqc.metrics.tsv","tests/fixtures/rna_calling/SAMPLE_002.rnaseqc.metrics.tsv"],"outputs":["tests/fixtures/rna_calling/expected/SAMPLE_001.strand.txt","tests/fixtures/rna_calling/expected/fastq.list.trimmed.txt","tests/fixtures/rna_calling/expected/rnaseqc.rnaseqc.exon_readsCount.gct.gz","tests/fixtures/rna_calling/expected/rnaseqc.rnaseqc.gene_readsCount.gct.gz","tests/fixtures/rna_calling/expected/rnaseqc.rnaseqc.gene_tpm.gct.gz","tests/fixtures/rna_calling/expected/rnaseqc.rnaseqc.metrics.tsv"],"files":["tests/fixtures/rna_calling/protocol_example.rnaseq.fastq.list.txt","tests/fixtures/rna_calling/SAMPLE_001.rnaseqc.metrics.tsv","tests/fixtures/rna_calling/SAMPLE_002.rnaseqc.metrics.tsv","tests/fixtures/rna_calling/expected/SAMPLE_001.strand.txt","tests/fixtures/rna_calling/expected/fastq.list.trimmed.txt","tests/fixtures/rna_calling/expected/rnaseqc.rnaseqc.exon_readsCount.gct.gz","tests/fixtures/rna_calling/expected/rnaseqc.rnaseqc.gene_readsCount.gct.gz","tests/fixtures/rna_calling/expected/rnaseqc.rnaseqc.gene_tpm.gct.gz","tests/fixtures/rna_calling/expected/rnaseqc.rnaseqc.metrics.tsv"]},"SuSiE_enloc":{"dir":"tests/fixtures/susie_enloc","dirs":["tests/fixtures/susie_enloc","tests/fixtures/susie_enloc/expected"],"inputs":["tests/fixtures/susie_enloc/protocol_example.enloc.gwas_meta.tsv","tests/fixtures/susie_enloc/protocol_example.enloc.xqtl_meta.tsv"],"outputs":["tests/fixtures/susie_enloc/expected/coloc.rds","tests/fixtures/susie_enloc/expected/colocboost.rds","tests/fixtures/susie_enloc/expected/colocboost_manifest.tsv","tests/fixtures/susie_enloc/expected/enloc_manifest.enrichment.tsv","tests/fixtures/susie_enloc/expected/enloc_manifest.coloc.tsv"],"files":["tests/fixtures/susie_enloc/protocol_example.enloc.gwas_meta.tsv","tests/fixtures/susie_enloc/protocol_example.enloc.xqtl_meta.tsv","tests/fixtures/susie_enloc/expected/coloc.rds","tests/fixtures/susie_enloc/expected/colocboost.rds","tests/fixtures/susie_enloc/expected/colocboost_manifest.tsv","tests/fixtures/susie_enloc/expected/enloc_manifest.enrichment.tsv","tests/fixtures/susie_enloc/expected/enloc_manifest.coloc.tsv"]},"VCF_QC":{"dir":"tests/fixtures/vcf_qc","dirs":["tests/fixtures/vcf_qc","tests/fixtures/vcf_qc/expected"],"inputs":["tests/fixtures/vcf_qc/numeric_chr22.vcf.gz","tests/fixtures/vcf_qc/genotype.chr22_48M.vcf.gz"],"outputs":["tests/fixtures/vcf_qc/expected/rename_chrs.variants.tsv","tests/fixtures/vcf_qc/expected/qc_normalize.variants.tsv","tests/fixtures/vcf_qc/expected/qc_2.variants.tsv","tests/fixtures/vcf_qc/expected/qc_3.novel.tstv","tests/fixtures/vcf_qc/expected/qc_3.known.tstv"],"files":["tests/fixtures/vcf_qc/numeric_chr22.vcf.gz","tests/fixtures/vcf_qc/genotype.chr22_48M.vcf.gz","tests/fixtures/vcf_qc/expected/rename_chrs.variants.tsv","tests/fixtures/vcf_qc/expected/qc_normalize.variants.tsv","tests/fixtures/vcf_qc/expected/qc_2.variants.tsv","tests/fixtures/vcf_qc/expected/qc_3.novel.tstv","tests/fixtures/vcf_qc/expected/qc_3.known.tstv"]},"apa_calling":{"dir":"tests/fixtures/apa_calling","dirs":["tests/fixtures/apa_calling"],"inputs":["tests/fixtures/apa_calling/depth.txt","tests/fixtures/apa_calling/chr22_3UTR.bed","tests/fixtures/apa_calling/chr22.hdr.gtf.gz"],"outputs":["tests/fixtures/apa_calling/expected_3UTR.bed","tests/fixtures/apa_calling/expected_gene_annotation.bed","tests/fixtures/apa_calling/expected_pdui_data.txt","tests/fixtures/apa_calling/expected_transcript_to_geneName.txt"],"files":["tests/fixtures/apa_calling/depth.txt","tests/fixtures/apa_calling/chr22_3UTR.bed","tests/fixtures/apa_calling/chr22.hdr.gtf.gz","tests/fixtures/apa_calling/expected_3UTR.bed","tests/fixtures/apa_calling/expected_gene_annotation.bed","tests/fixtures/apa_calling/expected_pdui_data.txt","tests/fixtures/apa_calling/expected_transcript_to_geneName.txt"]},"apa_impute":{"dir":"tests/fixtures/apa_impute","dirs":["tests/fixtures/apa_impute","tests/fixtures/apa_impute/apa_chr22","tests/fixtures/apa_impute/expected"],"inputs":["tests/fixtures/apa_impute/protocol_example.apa_matchtable.txt","tests/fixtures/apa_impute/apa_chr22/Dapars_result_result_temp.chr22.txt"],"outputs":["tests/fixtures/apa_impute/expected/expected.Dapars_result_impute_chr22.bed","tests/fixtures/apa_impute/expected/expected.Dapars_allchrom.bed","tests/fixtures/apa_impute/expected/expected.Dapars_result_impute_renamed_chr22.bed.gz","tests/fixtures/apa_impute/expected/expected.Dapars_allchrom_renamed.bed"],"files":["tests/fixtures/apa_impute/protocol_example.apa_matchtable.txt","tests/fixtures/apa_impute/apa_chr22/Dapars_result_result_temp.chr22.txt","tests/fixtures/apa_impute/expected/expected.Dapars_result_impute_chr22.bed","tests/fixtures/apa_impute/expected/expected.Dapars_allchrom.bed","tests/fixtures/apa_impute/expected/expected.Dapars_result_impute_renamed_chr22.bed.gz","tests/fixtures/apa_impute/expected/expected.Dapars_allchrom_renamed.bed"]},"bulk_expression_normalization":{"dir":"tests/fixtures/bulk_expression_normalization","dirs":["tests/fixtures/bulk_expression_normalization","tests/fixtures/bulk_expression_normalization/expected"],"inputs":["tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.geneCount.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.sample_participant_lookup.txt"],"outputs":["tests/fixtures/bulk_expression_normalization/expected/expected.qc_1.low_expression_filtered.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_2.outlier_removed.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_3.outlier_removed.geneCount.gct.gz"],"files":["tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.geneCount.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.sample_participant_lookup.txt","tests/fixtures/bulk_expression_normalization/expected/expected.qc_1.low_expression_filtered.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_2.outlier_removed.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_3.outlier_removed.geneCount.gct.gz"]},"colocboost":{"dir":"tests/fixtures/colocboost/expected","dirs":["tests/fixtures/colocboost/expected","tests/fixtures/qtl_mini"],"inputs":["tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bed","tests/fixtures/qtl_mini/protocol_example.pheno_manifest_context.tsv","tests/fixtures/qtl_mini/example_covariates.tsv","tests/fixtures/qtl_mini/association_windows.bed"],"outputs":["tests/fixtures/colocboost/expected/test_coloc.ENSG00000283047.colocboost.rds"],"files":["tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bed","tests/fixtures/qtl_mini/protocol_example.pheno_manifest_context.tsv","tests/fixtures/qtl_mini/example_covariates.tsv","tests/fixtures/qtl_mini/association_windows.bed","tests/fixtures/colocboost/expected/test_coloc.ENSG00000283047.colocboost.rds"]},"covariate_formatting":{"dir":"tests/fixtures/covariate_formatting","dirs":["tests/fixtures/covariate_formatting","tests/fixtures/covariate_formatting/expected"],"inputs":["tests/fixtures/covariate_formatting/covariates.base.tsv"],"outputs":["tests/fixtures/covariate_formatting/expected/merged.gz"],"files":["tests/fixtures/covariate_formatting/covariates.base.tsv","tests/fixtures/covariate_formatting/expected/merged.gz"]},"covariate_hidden_factor":{"dir":"tests/fixtures/covariate_hidden_factor","dirs":["tests/fixtures/covariate_hidden_factor","tests/fixtures/covariate_hidden_factor/expected"],"inputs":["tests/fixtures/covariate_hidden_factor/covariates.tsv"],"outputs":["tests/fixtures/covariate_hidden_factor/expected/residual.bed.gz","tests/fixtures/covariate_hidden_factor/expected/Marchenko_PC.gz","tests/fixtures/covariate_hidden_factor/expected/Buja_Eyuboglu_PC.gz","tests/fixtures/covariate_hidden_factor/expected/PEER.factors.tsv","tests/fixtures/covariate_hidden_factor/expected/PEER.weights.tsv","tests/fixtures/covariate_hidden_factor/expected/PEER.variance.tsv","tests/fixtures/covariate_hidden_factor/expected/PEER.gz"],"files":["tests/fixtures/covariate_hidden_factor/covariates.tsv","tests/fixtures/covariate_hidden_factor/expected/residual.bed.gz","tests/fixtures/covariate_hidden_factor/expected/Marchenko_PC.gz","tests/fixtures/covariate_hidden_factor/expected/Buja_Eyuboglu_PC.gz","tests/fixtures/covariate_hidden_factor/expected/PEER.factors.tsv","tests/fixtures/covariate_hidden_factor/expected/PEER.weights.tsv","tests/fixtures/covariate_hidden_factor/expected/PEER.variance.tsv","tests/fixtures/covariate_hidden_factor/expected/PEER.gz"]},"ems_prediction":{"dir":"tests/fixtures/ems_training","dirs":["tests/fixtures/ems_training","tests/fixtures/ems_training/expected"],"inputs":["tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr1.tsv","tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr2.tsv","tests/fixtures/ems_training/model_config.yaml"],"outputs":["tests/fixtures/ems_training/expected/features_importance_model5_chr_chr2_NPR_1.csv","tests/fixtures/ems_training/expected/model_5_summary_chr_chr2_NPR_1.json","tests/fixtures/ems_training/expected/predictions_weighted_model_chr2.tsv"],"files":["tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr1.tsv","tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr2.tsv","tests/fixtures/ems_training/model_config.yaml","tests/fixtures/ems_training/expected/features_importance_model5_chr_chr2_NPR_1.csv","tests/fixtures/ems_training/expected/model_5_summary_chr_chr2_NPR_1.json","tests/fixtures/ems_training/expected/predictions_weighted_model_chr2.tsv"]},"ems_training":{"dir":"tests/fixtures/ems_training","dirs":["tests/fixtures/ems_training","tests/fixtures/ems_training/expected"],"inputs":["tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr1.tsv","tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr2.tsv","tests/fixtures/ems_training/model_config.yaml"],"outputs":["tests/fixtures/ems_training/expected/features_importance_model5_chr_chr2_NPR_1.csv","tests/fixtures/ems_training/expected/model_5_summary_chr_chr2_NPR_1.json","tests/fixtures/ems_training/expected/predictions_weighted_model_chr2.tsv"],"files":["tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr1.tsv","tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr2.tsv","tests/fixtures/ems_training/model_config.yaml","tests/fixtures/ems_training/expected/features_importance_model5_chr_chr2_NPR_1.csv","tests/fixtures/ems_training/expected/model_5_summary_chr_chr2_NPR_1.json","tests/fixtures/ems_training/expected/predictions_weighted_model_chr2.tsv"]},"eoo_enrichment":{"dir":"tests/fixtures/eoo_enrichment","dirs":["tests/fixtures/eoo_enrichment","tests/fixtures/eoo_enrichment/expected"],"inputs":["tests/fixtures/eoo_enrichment/protocol_example.eoo_baseline_annotation.tsv.gz","tests/fixtures/eoo_enrichment/protocol_example.eoo_significant_variants.tsv.gz"],"outputs":["tests/fixtures/eoo_enrichment/expected/enrichment_results.rds","tests/fixtures/eoo_enrichment/expected/enrichment_results_summary.tsv.gz"],"files":["tests/fixtures/eoo_enrichment/protocol_example.eoo_baseline_annotation.tsv.gz","tests/fixtures/eoo_enrichment/protocol_example.eoo_significant_variants.tsv.gz","tests/fixtures/eoo_enrichment/expected/enrichment_results.rds","tests/fixtures/eoo_enrichment/expected/enrichment_results_summary.tsv.gz"]},"gene_annotation":{"dir":"tests/fixtures/gene_annotation","dirs":["tests/fixtures/gene_annotation","tests/fixtures/gene_annotation/expected"],"inputs":["tests/fixtures/gene_annotation/protocol_example.atac.tsv","tests/fixtures/gene_annotation/protocol_example.rnaseq.bed.gz"],"outputs":["tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.gene_list.tsv","tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.region_list.txt","tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.gene_list.tsv","tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.region_list.txt","tests/fixtures/gene_annotation/expected/protocol_example.atac.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.atac.region_list.txt","tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.intron_count.tsv.leafcutter.clusters_to_genes.txt","tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.phenotype.bed.formated.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.phenotype.bed.phenotype_group.txt","tests/fixtures/gene_annotation/expected/protocol_example.psichomics.phenotype.formated.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.psichomics.phenotype.phenotype_group.txt"],"files":["tests/fixtures/gene_annotation/protocol_example.atac.tsv","tests/fixtures/gene_annotation/protocol_example.rnaseq.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.gene_list.tsv","tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.region_list.txt","tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.gene_list.tsv","tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.region_list.txt","tests/fixtures/gene_annotation/expected/protocol_example.atac.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.atac.region_list.txt","tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.intron_count.tsv.leafcutter.clusters_to_genes.txt","tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.phenotype.bed.formated.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.phenotype.bed.phenotype_group.txt","tests/fixtures/gene_annotation/expected/protocol_example.psichomics.phenotype.formated.bed.gz","tests/fixtures/gene_annotation/expected/protocol_example.psichomics.phenotype.phenotype_group.txt"]},"generalized_TADB":{"dir":"tests/fixtures/generalized_TADB","dirs":["tests/fixtures/generalized_TADB","tests/fixtures/generalized_TADB/expected"],"inputs":["tests/fixtures/generalized_TADB/protocol_example.brain_TADs.txt","tests/fixtures/generalized_TADB/protocol_example.gene_start_end.tsv"],"outputs":["tests/fixtures/generalized_TADB/expected/generalized_TAD.tsv","tests/fixtures/generalized_TADB/expected/generalized_TADB.tsv","tests/fixtures/generalized_TADB/expected/TADB_enhanced_cis.bed","tests/fixtures/generalized_TADB/expected/extended_TADB.bed"],"files":["tests/fixtures/generalized_TADB/protocol_example.brain_TADs.txt","tests/fixtures/generalized_TADB/protocol_example.gene_start_end.tsv","tests/fixtures/generalized_TADB/expected/generalized_TAD.tsv","tests/fixtures/generalized_TADB/expected/generalized_TADB.tsv","tests/fixtures/generalized_TADB/expected/TADB_enhanced_cis.bed","tests/fixtures/generalized_TADB/expected/extended_TADB.bed"]},"genotype_formatting":{"dir":"tests/fixtures/genotype_formatting","dirs":["tests/fixtures/genotype_formatting/geno","tests/fixtures/genotype_formatting/expected"],"inputs":["tests/fixtures/genotype_formatting/geno/chr21.bed","tests/fixtures/genotype_formatting/geno/chr21.bim"],"outputs":["tests/fixtures/genotype_formatting/expected/ld_by_region.float16.rds","tests/fixtures/genotype_formatting/expected/plink_to_vcf.variants.tsv","tests/fixtures/genotype_formatting/expected/vcf_to_plink.bim","tests/fixtures/genotype_formatting/expected/genotype_by_region.bim","tests/fixtures/genotype_formatting/expected/genotype_by_chrom.bim"],"files":["tests/fixtures/genotype_formatting/geno/chr21.bed","tests/fixtures/genotype_formatting/geno/chr21.bim","tests/fixtures/genotype_formatting/expected/ld_by_region.float16.rds","tests/fixtures/genotype_formatting/expected/plink_to_vcf.variants.tsv","tests/fixtures/genotype_formatting/expected/vcf_to_plink.bim","tests/fixtures/genotype_formatting/expected/genotype_by_region.bim","tests/fixtures/genotype_formatting/expected/genotype_by_chrom.bim"]},"gregor":{"dir":"tests/fixtures/gregor","dirs":["tests/fixtures/gregor","tests/fixtures/gregor/expected"],"inputs":["tests/fixtures/gregor/index.snps.txt","tests/fixtures/gregor/test_peaks.bed","tests/fixtures/gregor/example_enrichment_results.txt"],"outputs":["tests/fixtures/gregor/expected/enrichment_results.txt"],"files":["tests/fixtures/gregor/index.snps.txt","tests/fixtures/gregor/test_peaks.bed","tests/fixtures/gregor/example_enrichment_results.txt","tests/fixtures/gregor/expected/enrichment_results.txt"]},"gsea":{"dir":"tests/fixtures/gsea","dirs":["tests/fixtures/gsea","tests/fixtures/gsea/expected"],"inputs":["tests/fixtures/gsea/protocol_example.pathway_genes.tsv"],"outputs":["tests/fixtures/gsea/expected/pathway_go_results.rds"],"files":["tests/fixtures/gsea/protocol_example.pathway_genes.tsv","tests/fixtures/gsea/expected/pathway_go_results.rds"]},"intact":{"dir":"tests/fixtures/intact","dirs":["tests/fixtures/intact","tests/fixtures/intact/expected"],"inputs":["tests/fixtures/intact/README.md","tests/fixtures/intact/protocol_example.ptwas.output"],"outputs":["tests/fixtures/intact/expected/intact.rds"],"files":["tests/fixtures/intact/README.md","tests/fixtures/intact/protocol_example.ptwas.output","tests/fixtures/intact/expected/intact.rds"]},"ld_prune_reference":{"dir":"tests/fixtures/ld_prune_reference/expected","dirs":["tests/fixtures/ld_prune_reference/expected","tests/fixtures/ld_prune_reference/genotype"],"inputs":["tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.bed","tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.bim","tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.fam"],"outputs":["tests/fixtures/ld_prune_reference/expected/LD_pruned_variants.txt"],"files":["tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.bed","tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.bim","tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.fam","tests/fixtures/ld_prune_reference/expected/LD_pruned_variants.txt"]},"mash_fit":{"dir":"tests/fixtures/mash","dirs":["tests/fixtures/mash","tests/fixtures/mash/expected"],"inputs":["tests/fixtures/mash/mashr_input.rds","tests/fixtures/mash/region_strong.rds","tests/fixtures/mash/Ast_De_Jager_eQTL.tsv"],"outputs":["tests/fixtures/mash/expected/mash_model.EE.rds"],"files":["tests/fixtures/mash/mashr_input.rds","tests/fixtures/mash/region_strong.rds","tests/fixtures/mash/Ast_De_Jager_eQTL.tsv","tests/fixtures/mash/expected/mash_model.EE.rds"]},"mash_posterior":{"dir":"tests/fixtures/mash_posterior","dirs":["tests/fixtures/mash_posterior"],"inputs":["tests/fixtures/mash_posterior/orig.rds","tests/fixtures/mash_posterior/posterior.rds","tests/fixtures/mash_posterior/fine_mapping.rds"],"outputs":["tests/fixtures/mash_posterior/fine_mapping.rds","tests/fixtures/mash_posterior/orig.rds","tests/fixtures/mash_posterior/posterior.rds"],"files":["tests/fixtures/mash_posterior/orig.rds","tests/fixtures/mash_posterior/posterior.rds","tests/fixtures/mash_posterior/fine_mapping.rds","tests/fixtures/mash_posterior/fine_mapping.rds","tests/fixtures/mash_posterior/orig.rds","tests/fixtures/mash_posterior/posterior.rds"]},"mash_preprocessing":{"dir":"tests/fixtures/mash","dirs":["tests/fixtures/mash","tests/fixtures/mash/expected"],"inputs":["tests/fixtures/mash/mashr_input.rds","tests/fixtures/mash/region_strong.rds","tests/fixtures/mash/Ast_De_Jager_eQTL.tsv"],"outputs":["tests/fixtures/mash/expected/mash_sumstats.region1.rds","tests/fixtures/mash/expected/mash_input.qss.rds","tests/fixtures/mash/expected/mash_input.fmr.rds","tests/fixtures/mash/expected/mash_input.indep.rds"],"files":["tests/fixtures/mash/mashr_input.rds","tests/fixtures/mash/region_strong.rds","tests/fixtures/mash/Ast_De_Jager_eQTL.tsv","tests/fixtures/mash/expected/mash_sumstats.region1.rds","tests/fixtures/mash/expected/mash_input.qss.rds","tests/fixtures/mash/expected/mash_input.fmr.rds","tests/fixtures/mash/expected/mash_input.indep.rds"]},"mixture_prior":{"dir":"tests/fixtures/mash","dirs":["tests/fixtures/mash","tests/fixtures/mash/expected"],"inputs":["tests/fixtures/mash/mashr_input.rds","tests/fixtures/mash/region_strong.rds","tests/fixtures/mash/Ast_De_Jager_eQTL.tsv"],"outputs":["tests/fixtures/mash/expected/mixture_prior.EE.prior.rds","tests/fixtures/mash/expected/vhat.identity.EE.rds","tests/fixtures/mash/expected/vhat.simple.EE.rds","tests/fixtures/mash/expected/vhat.corshrink.EE.rds","tests/fixtures/mash/expected/vhat.simple_specific.EE.rds","tests/fixtures/mash/expected/prior.cov_ed.EE.rds","tests/fixtures/mash/expected/cov.canonical.EE.rds","tests/fixtures/mash/expected/cov.pca.EE.rds","tests/fixtures/mash/expected/cov.flash.EE.rds","tests/fixtures/mash/expected/cov.flash_nonneg.EE.rds"],"files":["tests/fixtures/mash/mashr_input.rds","tests/fixtures/mash/region_strong.rds","tests/fixtures/mash/Ast_De_Jager_eQTL.tsv","tests/fixtures/mash/expected/mixture_prior.EE.prior.rds","tests/fixtures/mash/expected/vhat.identity.EE.rds","tests/fixtures/mash/expected/vhat.simple.EE.rds","tests/fixtures/mash/expected/vhat.corshrink.EE.rds","tests/fixtures/mash/expected/vhat.simple_specific.EE.rds","tests/fixtures/mash/expected/prior.cov_ed.EE.rds","tests/fixtures/mash/expected/cov.canonical.EE.rds","tests/fixtures/mash/expected/cov.pca.EE.rds","tests/fixtures/mash/expected/cov.flash.EE.rds","tests/fixtures/mash/expected/cov.flash_nonneg.EE.rds"]},"phenotype_formatting":{"dir":"tests/fixtures/phenotype_formatting","dirs":["tests/fixtures/phenotype_formatting","tests/fixtures/phenotype_formatting/expected","tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region"],"inputs":["tests/fixtures/phenotype_formatting/regions.txt","tests/fixtures/phenotype_formatting/tad_list.txt","tests/fixtures/phenotype_formatting/keep_samples.txt"],"outputs":["tests/fixtures/phenotype_formatting/expected/protocol_example.chr22.bed.gz","tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_chrom_files.txt","tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_chrom_files.region_list.txt","tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region/protocol_example.region1.bed.gz","tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region/protocol_example.region2.bed.gz","tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_region_files.txt","tests/fixtures/phenotype_formatting/expected/protocol_example.tpm.sample_matched.gct.gz","tests/fixtures/phenotype_formatting/expected/protocol_example.rnaseq.bed.bed.gz.tad_list.txt.2_pheno_per_region.region_list","tests/fixtures/phenotype_formatting/expected/protocol_example.chr22.gct"],"files":["tests/fixtures/phenotype_formatting/regions.txt","tests/fixtures/phenotype_formatting/tad_list.txt","tests/fixtures/phenotype_formatting/keep_samples.txt","tests/fixtures/phenotype_formatting/expected/protocol_example.chr22.bed.gz","tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_chrom_files.txt","tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_chrom_files.region_list.txt","tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region/protocol_example.region1.bed.gz","tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region/protocol_example.region2.bed.gz","tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_region_files.txt","tests/fixtures/phenotype_formatting/expected/protocol_example.tpm.sample_matched.gct.gz","tests/fixtures/phenotype_formatting/expected/protocol_example.rnaseq.bed.bed.gz.tad_list.txt.2_pheno_per_region.region_list","tests/fixtures/phenotype_formatting/expected/protocol_example.chr22.gct"]},"phenotype_imputation":{"dir":"tests/fixtures/phenotype_imputation","dirs":["tests/fixtures/phenotype_imputation","tests/fixtures/phenotype_imputation/expected"],"inputs":["tests/fixtures/phenotype_imputation/protocol_example.protein.missing.bed.gz"],"outputs":["tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.EBMF.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.knn.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.mean.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.lod.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.soft.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.filtered.imputed.bed.gz"],"files":["tests/fixtures/phenotype_imputation/protocol_example.protein.missing.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.EBMF.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.knn.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.mean.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.lod.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.soft.imputed.bed.gz","tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.filtered.imputed.bed.gz"]},"pseudobulk_preprocessing":{"dir":"tests/fixtures/pseudobulk_preprocessing","dirs":["tests/fixtures/pseudobulk_preprocessing","tests/fixtures/pseudobulk_preprocessing/expected"],"inputs":["tests/fixtures/pseudobulk_preprocessing/protocol_example.snrnaseq.seurat_MIC.rds","tests/fixtures/pseudobulk_preprocessing/counts_MIC.csv.gz","tests/fixtures/pseudobulk_preprocessing/atac_MIC_residuals.txt"],"outputs":["tests/fixtures/pseudobulk_preprocessing/expected/expected_counts_MIC.remapped.csv.gz","tests/fixtures/pseudobulk_preprocessing/expected/expected_MIC_residuals_qn.txt"],"files":["tests/fixtures/pseudobulk_preprocessing/protocol_example.snrnaseq.seurat_MIC.rds","tests/fixtures/pseudobulk_preprocessing/counts_MIC.csv.gz","tests/fixtures/pseudobulk_preprocessing/atac_MIC_residuals.txt","tests/fixtures/pseudobulk_preprocessing/expected/expected_counts_MIC.remapped.csv.gz","tests/fixtures/pseudobulk_preprocessing/expected/expected_MIC_residuals_qn.txt"]},"qtl_association_postprocessing":{"dir":"tests/fixtures/qtl_association_postprocessing","dirs":["tests/fixtures/qtl_association_postprocessing","tests/fixtures/qtl_association_postprocessing/expected"],"inputs":["tests/fixtures/qtl_association_postprocessing/protocol_example.cis_qtl.pairs.tsv.gz","tests/fixtures/qtl_association_postprocessing/protocol_example.cis_qtl.regional.tsv.gz","tests/fixtures/qtl_association_postprocessing/protocol_example.maf_0.01_window_1000000_cis_n_variants_stats.tsv.gz"],"outputs":["tests/fixtures/qtl_association_postprocessing/expected/qap.rds","tests/fixtures/qtl_association_postprocessing/expected/qap.cis_regional.fdr.tsv.gz","tests/fixtures/qtl_association_postprocessing/expected/qap.summary.tsv"],"files":["tests/fixtures/qtl_association_postprocessing/protocol_example.cis_qtl.pairs.tsv.gz","tests/fixtures/qtl_association_postprocessing/protocol_example.cis_qtl.regional.tsv.gz","tests/fixtures/qtl_association_postprocessing/protocol_example.maf_0.01_window_1000000_cis_n_variants_stats.tsv.gz","tests/fixtures/qtl_association_postprocessing/expected/qap.rds","tests/fixtures/qtl_association_postprocessing/expected/qap.cis_regional.fdr.tsv.gz","tests/fixtures/qtl_association_postprocessing/expected/qap.summary.tsv"]},"reference_data_preparation":{"dir":"tests/fixtures/reference_data_preparation","dirs":["tests/fixtures/reference_data_preparation","tests/fixtures/reference_data_preparation/expected"],"inputs":["tests/fixtures/reference_data_preparation/hgnc_chr22.tsv.gz","tests/fixtures/reference_data_preparation/mini.gff3","tests/fixtures/reference_data_preparation/ERCC92.gtf"],"outputs":["tests/fixtures/reference_data_preparation/expected/hg_reference_1.filtered.fasta","tests/fixtures/reference_data_preparation/expected/hg_gtf_1.reformatted.gtf","tests/fixtures/reference_data_preparation/expected/faidx.test_contigs.fa.fai","tests/fixtures/reference_data_preparation/expected/mini.gtf","tests/fixtures/reference_data_preparation/expected/hg38.chr22_SE_strict.ioe","tests/fixtures/reference_data_preparation/expected/chr22.SUPPA_annotation.rds"],"files":["tests/fixtures/reference_data_preparation/hgnc_chr22.tsv.gz","tests/fixtures/reference_data_preparation/mini.gff3","tests/fixtures/reference_data_preparation/ERCC92.gtf","tests/fixtures/reference_data_preparation/expected/hg_reference_1.filtered.fasta","tests/fixtures/reference_data_preparation/expected/hg_gtf_1.reformatted.gtf","tests/fixtures/reference_data_preparation/expected/faidx.test_contigs.fa.fai","tests/fixtures/reference_data_preparation/expected/mini.gtf","tests/fixtures/reference_data_preparation/expected/hg38.chr22_SE_strict.ioe","tests/fixtures/reference_data_preparation/expected/chr22.SUPPA_annotation.rds"]},"rss_analysis":{"dir":"tests/fixtures/rss_analysis","dirs":["tests/fixtures/rss_analysis","tests/fixtures/rss_analysis/expected"],"inputs":["tests/fixtures/rss_analysis/protocol_example.rss_mwe.gwas_meta.tsv","tests/fixtures/rss_analysis/protocol_example.gwas_sumstats.chr22.tsv.gz","tests/fixtures/rss_analysis/protocol_example.gwas_column_mapping.yml"],"outputs":["tests/fixtures/rss_analysis/expected/gwas_sumstats.rds","tests/fixtures/rss_analysis/expected/gwas_finemap.rds"],"files":["tests/fixtures/rss_analysis/protocol_example.rss_mwe.gwas_meta.tsv","tests/fixtures/rss_analysis/protocol_example.gwas_sumstats.chr22.tsv.gz","tests/fixtures/rss_analysis/protocol_example.gwas_column_mapping.yml","tests/fixtures/rss_analysis/expected/gwas_sumstats.rds","tests/fixtures/rss_analysis/expected/gwas_finemap.rds"]},"rss_ld_sketch":{"dir":"tests/fixtures/rss_ld_sketch","dirs":["tests/fixtures/rss_ld_sketch","tests/fixtures/rss_ld_sketch/expected"],"inputs":["tests/fixtures/rss_ld_sketch/protocol_example.ld_blocks.bed","tests/fixtures/rss_ld_sketch/protocol_example.genotype.chr22.vcf.gz","tests/fixtures/rss_ld_sketch/protocol_example.genotype.chr22.vcf.gz.tbi"],"outputs":["tests/fixtures/rss_ld_sketch/expected/afreq_deterministic.tsv","tests/fixtures/rss_ld_sketch/expected/event_id.tsv"],"files":["tests/fixtures/rss_ld_sketch/protocol_example.ld_blocks.bed","tests/fixtures/rss_ld_sketch/protocol_example.genotype.chr22.vcf.gz","tests/fixtures/rss_ld_sketch/protocol_example.genotype.chr22.vcf.gz.tbi","tests/fixtures/rss_ld_sketch/expected/afreq_deterministic.tsv","tests/fixtures/rss_ld_sketch/expected/event_id.tsv"]},"sldsc_enrichment":{"dir":"tests/fixtures/sldsc_enrichment","dirs":["tests/fixtures/sldsc_enrichment","tests/fixtures/sldsc_enrichment/expected"],"inputs":["tests/fixtures/sldsc_enrichment/target.tsv","tests/fixtures/sldsc_enrichment/reference.2.bed","tests/fixtures/sldsc_enrichment/reference.2.bim"],"outputs":["tests/fixtures/sldsc_enrichment/expected/sldsc_postprocess.rds","tests/fixtures/sldsc_enrichment/expected/sldsc_meta_subset.rds","tests/fixtures/sldsc_enrichment/expected/sldsc_meta_subset.notebook.rds"],"files":["tests/fixtures/sldsc_enrichment/target.tsv","tests/fixtures/sldsc_enrichment/reference.2.bed","tests/fixtures/sldsc_enrichment/reference.2.bim","tests/fixtures/sldsc_enrichment/expected/sldsc_postprocess.rds","tests/fixtures/sldsc_enrichment/expected/sldsc_meta_subset.rds","tests/fixtures/sldsc_enrichment/expected/sldsc_meta_subset.notebook.rds"]},"snRNAseq_preprocessing":{"dir":"tests/fixtures/snrnaseq_preprocessing","dirs":["tests/fixtures/snrnaseq_preprocessing","tests/fixtures/snrnaseq_preprocessing/expected"],"inputs":["tests/fixtures/snrnaseq_preprocessing/protocol_example.snrnaseq.seurat_ref_SE.rds","tests/fixtures/snrnaseq_preprocessing/protocol_example.snrnaseq.id_mapping.csv"],"outputs":["tests/fixtures/snrnaseq_preprocessing/expected/expected_manifest.tsv"],"files":["tests/fixtures/snrnaseq_preprocessing/protocol_example.snrnaseq.seurat_ref_SE.rds","tests/fixtures/snrnaseq_preprocessing/protocol_example.snrnaseq.id_mapping.csv","tests/fixtures/snrnaseq_preprocessing/expected/expected_manifest.tsv"]},"splicing_calling":{"dir":"tests/fixtures/splicing_calling","dirs":["tests/fixtures/splicing_calling/leafcutter","tests/fixtures/splicing_calling/psichomics"],"inputs":["tests/fixtures/splicing_calling/leafcutter/SAMPLE_001.junc.gz","tests/fixtures/splicing_calling/leafcutter/SAMPLE_002.junc.gz"],"outputs":["tests/fixtures/splicing_calling/psichomics/expected_junctions.txt"],"files":["tests/fixtures/splicing_calling/leafcutter/SAMPLE_001.junc.gz","tests/fixtures/splicing_calling/leafcutter/SAMPLE_002.junc.gz","tests/fixtures/splicing_calling/psichomics/expected_junctions.txt"]},"splicing_normalization":{"dir":"tests/fixtures/splicing_normalization","dirs":["tests/fixtures/splicing_normalization","tests/fixtures/splicing_normalization/expected"],"inputs":["tests/fixtures/splicing_normalization/raw_data.txt.gz","tests/fixtures/splicing_normalization/psi_raw_data.tsv.gz"],"outputs":["tests/fixtures/splicing_normalization/expected.phen_chr22.gz","tests/fixtures/splicing_normalization/expected/expected.prepare_phenotype.ave","tests/fixtures/splicing_normalization/expected/expected.prepare_phenotype.phenotype_file_list.txt"],"files":["tests/fixtures/splicing_normalization/raw_data.txt.gz","tests/fixtures/splicing_normalization/psi_raw_data.tsv.gz","tests/fixtures/splicing_normalization/expected.phen_chr22.gz","tests/fixtures/splicing_normalization/expected/expected.prepare_phenotype.ave","tests/fixtures/splicing_normalization/expected/expected.prepare_phenotype.phenotype_file_list.txt"]},"twas_ctwas":{"dir":"tests/fixtures/twas","dirs":["tests/fixtures/twas","tests/fixtures/twas/expected"],"inputs":["tests/fixtures/twas/protocol_example.twas.gwas_meta.tsv","tests/fixtures/twas/protocol_example.twas.xqtl_meta.tsv"],"outputs":["tests/fixtures/twas/expected/gwas_sumstats.chr22.rds","tests/fixtures/twas/expected/twas.chr22.rds"],"files":["tests/fixtures/twas/protocol_example.twas.gwas_meta.tsv","tests/fixtures/twas/protocol_example.twas.xqtl_meta.tsv","tests/fixtures/twas/expected/gwas_sumstats.chr22.rds","tests/fixtures/twas/expected/twas.chr22.rds"]},"TensorQTL":{"dir":"tests/fixtures","dirs":["tests/fixtures/qtl_mini","tests/fixtures/tensorqtl/expected"],"inputs":["tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bed","tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bim","tests/fixtures/qtl_mini/protocol_example.genotype.chr22.fam","tests/fixtures/qtl_mini/example_geneexpr.bed.gz","tests/fixtures/qtl_mini/example_covariates.tsv","tests/fixtures/qtl_mini/association_windows.bed"],"outputs":["tests/fixtures/tensorqtl/expected/cis_qtl.pairs.tsv.gz","tests/fixtures/tensorqtl/expected/cis_qtl.regional.tsv.gz"],"files":["tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bed","tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bim","tests/fixtures/qtl_mini/protocol_example.genotype.chr22.fam","tests/fixtures/qtl_mini/example_geneexpr.bed.gz","tests/fixtures/qtl_mini/example_covariates.tsv","tests/fixtures/qtl_mini/association_windows.bed","tests/fixtures/tensorqtl/expected/cis_qtl.pairs.tsv.gz","tests/fixtures/tensorqtl/expected/cis_qtl.regional.tsv.gz"]},"bulk_expression_QC":{"dir":"tests/fixtures/bulk_expression_normalization","dirs":["tests/fixtures/bulk_expression_normalization","tests/fixtures/bulk_expression_normalization/expected"],"inputs":["tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.geneCount.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.sample_participant_lookup.txt"],"outputs":["tests/fixtures/bulk_expression_normalization/expected/expected.qc_1.low_expression_filtered.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_2.outlier_removed.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_3.outlier_removed.geneCount.gct.gz"],"files":["tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.geneCount.gct.gz","tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.sample_participant_lookup.txt","tests/fixtures/bulk_expression_normalization/expected/expected.qc_1.low_expression_filtered.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_2.outlier_removed.tpm.gct.gz","tests/fixtures/bulk_expression_normalization/expected/expected.qc_3.outlier_removed.geneCount.gct.gz"]},"mnm_regression":{"dir":"tests/fixtures/mnm_regression/expected","dirs":["tests/fixtures/mnm_regression/expected","tests/fixtures/qtl_mini"],"inputs":["tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bed","tests/fixtures/qtl_mini/protocol_example.pheno_manifest_context.tsv","tests/fixtures/qtl_mini/example_covariates.tsv","tests/fixtures/qtl_mini/association_windows.bed"],"outputs":["tests/fixtures/mnm_regression/expected/univariate_bvsr.rds","tests/fixtures/mnm_regression/expected/univariate_twas_weights.rds","tests/fixtures/mnm_regression/expected/protocol_example.ENSG00000283047.multicontext_bvsr.rds"],"files":["tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bed","tests/fixtures/qtl_mini/protocol_example.pheno_manifest_context.tsv","tests/fixtures/qtl_mini/example_covariates.tsv","tests/fixtures/qtl_mini/association_windows.bed","tests/fixtures/mnm_regression/expected/univariate_bvsr.rds","tests/fixtures/mnm_regression/expected/univariate_twas_weights.rds","tests/fixtures/mnm_regression/expected/protocol_example.ENSG00000283047.multicontext_bvsr.rds"]}},PREVIEWS={"tests/fixtures/gwas_qc/protocol_example.pheno.bed":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","1","2","G1","0.1","0.1","0.1","0.1"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/gwas_qc/protocol_example.kin0":{"kind":"table","rows":[["#FID1","IID1","FID2","IID2","NSNP","HETHET","IBS0","KINSHIP"],["0","SAMPLE_019","0","SAMPLE_008","3017","0.0775605","0.0215446","0.0713166"],["0","SAMPLE_038","0","SAMPLE_002","2966","0.0795684","0.0229265","0.062709"],["0","SAMPLE_040","0","SAMPLE_002","2952","0.0785908","0.0254065","0.062986"]],"shownColumns":8,"totalColumns":8,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/king.kin0":{"kind":"table","rows":[["#FID1","IID1","FID2","IID2","NSNP","HETHET","IBS0","KINSHIP"],["0","SAMPLE_019","0","SAMPLE_008","3017","0.0775605","0.0215446","0.0713166"],["0","SAMPLE_038","0","SAMPLE_002","2966","0.0795684","0.0229265","0.062709"],["0","SAMPLE_040","0","SAMPLE_002","2952","0.0785908","0.0254065","0.062986"]],"shownColumns":8,"totalColumns":8,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/king_2.related_id":{"kind":"table","rows":[["0","SAMPLE_038"],["0","SAMPLE_040"],["0","SAMPLE_041"],["0","SAMPLE_048"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/king_split.unrelated.fam":{"kind":"table","rows":[["0","SAMPLE_006","0","0","0","-9"],["0","SAMPLE_007","0","0","0","-9"],["0","SAMPLE_008","0","0","0","-9"],["0","SAMPLE_009","0","0","0","-9"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/king_split.related.fam":{"kind":"table","rows":[["0","SAMPLE_001","0","0","0","-9"],["0","SAMPLE_002","0","0","0","-9"],["0","SAMPLE_003","0","0","0","-9"],["0","SAMPLE_004","0","0","0","-9"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/qc_no_prune.bim":{"kind":"table","rows":[["22","chr22:10685239_C_T","0","10685239","T","C"],["22","chr22:10761227_G_A","0","10761227","A","G"],["22","chr22:11285239_C_T","0","11285239","T","C"],["22","chr22:11601805_G_A","0","11601805","A","G"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/qc_ld_prune.prune.in":{"kind":"table","rows":[["chr22:10761227_G_A"],["chr22:10859684_C_G"],["chr22:11271327_T_C"],["chr22:11285239_C_T"]],"shownColumns":1,"totalColumns":1,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/qc_ld_prune.bim":{"kind":"table","rows":[["22","chr22:10761227_G_A","0","10761227","A","G"],["22","chr22:10859684_C_G","0","10859684","G","C"],["22","chr22:11271327_T_C","0","11271327","C","T"],["22","chr22:11285239_C_T","0","11285239","T","C"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/sample_overlap.txt":{"kind":"table","rows":[["genotype_id","sample_id"],["SAMPLE_001","SAMPLE_001"],["SAMPLE_002","SAMPLE_002"],["SAMPLE_003","SAMPLE_003"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/gwas_qc/expected/king_workflow.unrelated.fam":{"kind":"table","rows":[["0","SAMPLE_001","0","0","0","-9"],["0","SAMPLE_002","0","0","0","-9"],["0","SAMPLE_003","0","0","0","-9"],["0","SAMPLE_004","0","0","0","-9"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/pca/protocol_example.pca_pheno.txt":{"kind":"table","rows":[["FID","IID","msex","age_death","pmi","study","race"],["SAMPLE_001","SAMPLE_001","1","90.97","10.57","1","1"],["SAMPLE_002","SAMPLE_002","1","80.24","7.87","0","1"],["SAMPLE_003","SAMPLE_003","1","83.9","9.93","0","1"]],"shownColumns":7,"totalColumns":7,"truncatedColumns":false},"tests/fixtures/pca/expected/project_samples.rds":{"kind":"rds","lines":["Object: list [length 6]"," Components: pca_model, pc_scores, meta, pc_cov, pc_mean, pc_median","$pca_model: flashpca [length 7]"," Components: values, vectors, projection, loadings, center, scale, pve","$pc_scores: data.frame [118 x 28]"," ID FID IID MID PID SEX"," 1 SAMPLE_001:SAMPLE_001 SAMPLE_001 SAMPLE_001 0 0 0"," 2 SAMPLE_002:SAMPLE_002 SAMPLE_002 SAMPLE_002 0 0 0"," 3 SAMPLE_003:SAMPLE_003 SAMPLE_003 SAMPLE_003 0 0 0","","$meta: character [length 1]"," Values: \"protocol_example.unrelated.prune \"","$pc_cov: matrix/array [5 x 5]"," [,1] [,2] [,3] [,4] [,5]"," [1,] 2.723426e-02 8.339899e-19 9.452205e-18 -3.973604e-18 2.797100e-19"," [2,] 8.339899e-19 2.696550e-02 8.385917e-18 9.369324e-18 2.240701e-17"," [3,] 9.452205e-18 8.385917e-18 2.612153e-02 1.781369e-17 -1.472802e-18","","$pc_mean: numeric [length 5]"," Values: c(-8.82062784394987e-18, -3.01077430406822e-17, 2.72851421306183e-17, 1.83469059154157e-17, 4.39855308484967e-17)","$pc_median: numeric [length 5]"," Values: c(0.00602721681627851, -0.00488368656715891, -0.003213717717953, -0.0157996403619344, 0.012215640237604)"]},"tests/fixtures/pca/expected/detect_outliers.maha.rds":{"kind":"rds","lines":["Object: list [length 4]"," Components: pc, manh_dis_sq_cutoff, msg, outliers","$pc: data.frame [59 x 25]"," IID FID pop PC1 PC2 PC3"," 1 SAMPLE_001 SAMPLE_001 1 -0.01226109 -0.07562966 -0.06502774"," 2 SAMPLE_002 SAMPLE_002 1 -0.27276569 -0.13080698 0.02576653"," 3 SAMPLE_003 SAMPLE_003 1 -0.01342011 -0.05296450 0.01199865","","$manh_dis_sq_cutoff: numeric [length 1]"," Values: c(`97.5%` = 12.1527505435543)","$msg: character [length 1]"," Values: \"# protocol_example.unrelated.prune result summary\\n## Mahalanobis distance summary:\\n```\\n Min. 1st Qu. Median Mean 3rd Qu. Max. \\n 0.2622 2.9169 4.2592 4.9153 6.5099 15.5199 \\n```\\n The cut-off for outlier removal is set to: 12.1527505435543 and the number of individuals to remove is: 2 \\n The new sample size after outlier removal is: 57 \\n\"","$outliers: data.frame [2 x 2]"," FID IID"," 40 SAMPLE_040 SAMPLE_040"," 51 SAMPLE_051 SAMPLE_051"]},"tests/fixtures/pca/expected/detect_outliers.outliers.txt":{"kind":"table","rows":[["SAMPLE_040","SAMPLE_040"],["SAMPLE_051","SAMPLE_051"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/pca/expected/pca_plink.eigenvec":{"kind":"table","rows":[["#FID","IID","PC1","PC2","PC3","PC4","PC5","PC6"],["SAMPLE_001","SAMPLE_001","0.00975568","0.0604747","-0.0528306","-0.0341157","0.0780374","0.193927"],["SAMPLE_002","SAMPLE_002","0.217029","0.104595","0.0209335","-0.132771","-0.0285064","-0.188891"],["SAMPLE_003","SAMPLE_003","0.0106779","0.0423513","0.00974808","0.0217471","-0.246944","-0.16355"]],"shownColumns":8,"totalColumns":22,"truncatedColumns":true},"tests/fixtures/pca/expected/flashpca.eigenvalues.tsv":{"kind":"table","rows":[["component","value","pve"],["1","1.57958724525007","0.0268867862620996"],["2","1.56399922939302","0.0266214564097226"],["3","1.51504853915088","0.0257882471331346"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/rna_calling/protocol_example.rnaseq.fastq.list.txt":{"kind":"table","rows":[["ID","fq1","fq2","strand","read_length"],["SAMPLE_001","SAMPLE_001_R1.fastq.gz","SAMPLE_001_R2.fastq.gz","rf","100"],["SAMPLE_002","SAMPLE_002_R1.fastq.gz","SAMPLE_002_R2.fastq.gz","rf","100"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/rna_calling/SAMPLE_001.rnaseqc.metrics.tsv":{"kind":"table","rows":[["Sample","SAMPLE_001"],["Mapping Rate","0.95"],["Genes Detected","2"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/rna_calling/SAMPLE_002.rnaseqc.metrics.tsv":{"kind":"table","rows":[["Sample","SAMPLE_002"],["Mapping Rate","0.95"],["Genes Detected","3"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/susie_enloc/protocol_example.enloc.gwas_meta.tsv":{"kind":"table","rows":[["#chr","start","end","region_id","TSS","original_data","combined_data","combined_data_sumstats"],["chr1","17351816","20110062","chr1_17351816_20110062","NA","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_17351816_20110062.univariate_susie_rss.rds","protocol_example.enloc.gwas.chr1_17351816_20110062.cis_results_db.export.rds","protocol_example.enloc.gwas.chr1_17351816_20110062.cis_results_db.export_sumstats.rds"],["chr1","20110062","22020160","chr1_20110062_22020160","NA","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_20110062_22020160.univariate_susie_rss.rds","protocol_example.enloc.gwas.chr1_20110062_22020160.cis_results_db.export.rds","protocol_example.enloc.gwas.chr1_20110062_22020160.cis_results_db.export_sumstats.rds"],["chr1","22020160","24199848","chr1_22020160_24199848","NA","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds","protocol_example.enloc.gwas.chr1_22020160_24199848.cis_results_db.export.rds","protocol_example.enloc.gwas.chr1_22020160_24199848.cis_results_db.export_sumstats.rds"]],"shownColumns":8,"totalColumns":11,"truncatedColumns":true},"tests/fixtures/susie_enloc/protocol_example.enloc.xqtl_meta.tsv":{"kind":"table","rows":[["#chr","start","end","region_id","TSS","original_data","combined_data","combined_data_sumstats"],["chr1","20520000","24080000","ENSG00000142798","21937309","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds,protocol_example.enloc.KNIGHT_pQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.qtl.ENSG00000142798.cis_results_db.export.rds","protocol_example.enloc.qtl.ENSG00000142798.cis_results_db.export_sumstats.rds"]],"shownColumns":8,"totalColumns":13,"truncatedColumns":true},"tests/fixtures/susie_enloc/expected/coloc.rds":{"kind":"rds","lines":["Object: data.frame [120 x 17]"," study context trait method gwasStudy gwasMethod"," 1 MiGA_eQTL MiGA_GFM_eQTL ENSG00000142798 susie AD_Bellenguez_2022 susie_rss"," 2 MiGA_eQTL MiGA_GFM_eQTL ENSG00000142798 susie AD_Bellenguez_2022 susie_rss"," 3 MiGA_eQTL MiGA_GFM_eQTL ENSG00000142798 susie AD_Bellenguez_2022 susie_rss"]},"tests/fixtures/susie_enloc/expected/colocboost.rds":{"kind":"rds","lines":["Object: list [length 4]"," Components: xqtl_coloc, joint_gwas, separate_gwas, computing_time","$xqtl_coloc: colocboost [length 6]"," Components: cos_summary, vcp, cos_details, data_info, model_info, ucos_details","$joint_gwas: NULL [length 0]","$separate_gwas: NULL [length 0]","$computing_time: list [length 1]"," Components: Analysis"]},"tests/fixtures/susie_enloc/expected/colocboost_manifest.tsv":{"kind":"table","rows":[["region_id","gene_id","chr","start","end","ld_block","studies","gwas_tsvs"],["ENSG00000283047","ENSG00000283047","chr22","10439387","11461338","chr22:10439387-11461338","",""]],"shownColumns":8,"totalColumns":12,"truncatedColumns":true},"tests/fixtures/susie_enloc/expected/enloc_manifest.enrichment.tsv":{"kind":"table","rows":[["unit_id","qtl_files","gwas_files"],["MiGA_GTS_eQTL","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds"],["MiGA_SVZ_eQTL","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds"],["MiGA_THA_eQTL","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/susie_enloc/expected/enloc_manifest.coloc.tsv":{"kind":"table","rows":[["unit_id","qtl_files","gwas_files"],["MiGA_GTS_eQTL@ENSG00000142798","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds"],["MiGA_SVZ_eQTL@ENSG00000142798","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds"],["MiGA_THA_eQTL@ENSG00000142798","protocol_example.enloc.MiGA_eQTL.ENSG00000142798.univariate_susie_twas_weights.rds","protocol_example.enloc.RSS_QC_RAISS_imputed.chr1_22020160_24199848.univariate_susie_rss.rds"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/vcf_qc/numeric_chr22.vcf.gz":{"kind":"table","rows":[["##fileformat=VCFv4.2"],["##FILTER="],["##fileDate=20231023"],["##source=PLINKv1.90"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/vcf_qc/genotype.chr22_48M.vcf.gz":{"kind":"table","rows":[["##fileformat=VCFv4.2"],["##FILTER="],["##fileDate=20231023"],["##source=PLINKv1.90"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/vcf_qc/expected/rename_chrs.variants.tsv":{"kind":"table","rows":[["chr22","10526333","chr22:10526333_CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT_*","CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT","*"],["chr22","10526566","chr22:10526566_AC_*","AC","*"],["chr22","10657618","chr22:10657618_C_G","C","G"],["chr22","10684490","chr22:10684490_G_A","G","A"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/vcf_qc/expected/qc_normalize.variants.tsv":{"kind":"table","rows":[["chr22","48000321","chr22:48000321:GT:G","GT","G"],["chr22","48000321","chr22:48000321:G:GTT","G","GTT"],["chr22","48000321","chr22:48000321:G:GTTT","G","GTTT"],["chr22","48000321","chr22:48000321:G:GTTTT","G","GTTTT"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/vcf_qc/expected/qc_3.novel.tstv":{"kind":"table","rows":[["TS/TV","stats:"],["No","results","available","(empty","input?)"],["Hom/Het","stats:"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/vcf_qc/expected/qc_3.known.tstv":{"kind":"table","rows":[["TS/TV stats:"],["Sample ","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["Transitions ","28","23","23","20","24","24","27"],["Transversions ","4","5","4","4","4","5","6"]],"shownColumns":8,"totalColumns":62,"truncatedColumns":true},"tests/fixtures/apa_calling/depth.txt":{"kind":"table","rows":[["SAMPLE_001","12709"],["SAMPLE_002","14497"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/apa_calling/chr22_3UTR.bed":{"kind":"table","rows":[["chr22","16654066","16654076","ENST00000456726|NA|chr22|-","0","-"],["chr22","16669464","16669620","ENST00000457060|ANKRD62P1-PARP4P3|chr22|-","0","-"],["chr22","17116297","17121360","ENST00000331437|TMEM121B|chr22|-","0","-"],["chr22","17116299","17120143","ENST00000399875|TMEM121B|chr22|-","0","-"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/apa_calling/chr22.hdr.gtf.gz":{"kind":"table","rows":[["#!header1"],["#!header2"],["#!header3"],["#!header4"]],"shownColumns":1,"totalColumns":1,"truncatedColumns":false},"tests/fixtures/apa_impute/protocol_example.apa_matchtable.txt":{"kind":"table","rows":[["ProjID","SampleID"],["Sample001","SampleA"],["Sample002","SampleB"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/apa_impute/apa_chr22/Dapars_result_result_temp.chr22.txt":{"kind":"table","rows":[["Gene","fit_value","Predicted_Proximal_APA","Loci","output/apa/wig/SAMPLE_001_PDUI","output/apa/wig/SAMPLE_002_PDUI"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/apa_impute/expected/expected.Dapars_result_impute_chr22.bed":{"kind":"table","rows":[["#chr","start","end","Gene"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/apa_impute/expected/expected.Dapars_allchrom.bed":{"kind":"table","rows":[["#chr","start","end","Gene"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/apa_impute/expected/expected.Dapars_result_impute_renamed_chr22.bed.gz":{"kind":"table","rows":[["#chr","start","end","Gene"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/apa_impute/expected/expected.Dapars_allchrom_renamed.bed":{"kind":"table","rows":[["#chr","start","end","Gene"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.tpm.gct.gz":{"kind":"table","rows":[["#1.2"],["# 300 60 "],["gene_ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","4.46908614068004","3.6324384389436","0","0.926449274182614","8.44864560635242","16.3456237133014","4.07740959667351"]],"shownColumns":8,"totalColumns":61,"truncatedColumns":true},"tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.geneCount.gct.gz":{"kind":"table","rows":[["#1.2"],["# 300 60 "],["gene_ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","197","193","122","180","217","257","195"]],"shownColumns":8,"totalColumns":61,"truncatedColumns":true},"tests/fixtures/bulk_expression_normalization/protocol_example.rnaseq.sample_participant_lookup.txt":{"kind":"table","rows":[["sample_id","participant_id"],["SAMPLE_001","SAMPLE_001"],["SAMPLE_002","SAMPLE_002"],["SAMPLE_003","SAMPLE_003"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/bulk_expression_normalization/expected/expected.qc_1.low_expression_filtered.tpm.gct.gz":{"kind":"table","rows":[["#1.2"],["# 300 60"],["gene_ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","4.46908614068004","3.6324384389436","0","0.926449274182614","8.44864560635242","16.3456237133014","4.07740959667351"]],"shownColumns":8,"totalColumns":61,"truncatedColumns":true},"tests/fixtures/bulk_expression_normalization/expected/expected.qc_2.outlier_removed.tpm.gct.gz":{"kind":"table","rows":[["#1.2"],["# 300 54"],["gene_ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","4.46908614068004","3.6324384389436","0","0.926449274182614","8.44864560635242","16.3456237133014","4.07740959667351"]],"shownColumns":8,"totalColumns":55,"truncatedColumns":true},"tests/fixtures/bulk_expression_normalization/expected/expected.qc_3.outlier_removed.geneCount.gct.gz":{"kind":"table","rows":[["#1.2"],["# 300 54 "],["gene_ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","197","193","122","180","217","257","195"]],"shownColumns":8,"totalColumns":55,"truncatedColumns":true},"tests/fixtures/colocboost/expected/test_coloc.ENSG00000283047.colocboost.rds":{"kind":"rds","lines":["Object: list [length 4]"," Components: xqtl_coloc, joint_gwas, separate_gwas, computing_time","$xqtl_coloc: colocboost [length 6]"," Components: cos_summary, vcp, cos_details, data_info, model_info, ucos_details","$joint_gwas: NULL [length 0]","$separate_gwas: NULL [length 0]","$computing_time: list [length 1]"," Components: Analysis"]},"tests/fixtures/covariate_formatting/covariates.base.tsv":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","1","1","0","0"],["age","90.97","80.24","83.9","74.1","93.94","89.95","91.39"]],"shownColumns":8,"totalColumns":61,"truncatedColumns":true},"tests/fixtures/covariate_formatting/expected/merged.gz":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","1","1","0","0"],["age","90.97","80.24","83.9","74.1","93.94","89.95","91.39"],["PC1","-0.012261092152600217","-0.27276568851005745","-0.013420106161445802","0.11884720720763796","0.006027216816278508","0.16975817747495048","-0.176420328093058"]],"shownColumns":8,"totalColumns":60,"truncatedColumns":true},"tests/fixtures/covariate_hidden_factor/covariates.tsv":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","0","1","0","1"],["age","67.06","82.92","87.76","64.57","81.62","66.44","75.53"],["PC1","-0.7904","-0.1993","0.3059","2.1952","-0.0345","-0.4571","0.7942"]],"shownColumns":8,"totalColumns":50,"truncatedColumns":true},"tests/fixtures/covariate_hidden_factor/expected/residual.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","10939387","10961337","ENSG00000283047","29.946170491386496","-8.44968773314525","-1.7767246013041644","-3.7499243841617105"],["chr22","15528191","15529138","ENSG00000130538","-2.9173358185760385","-5.007200781431884","-0.29519619760879173","3.938154273806503"],["chr22","15611758","15613095","ENSG00000231565","2.85916554775662","-4.676226628425212","-1.6400806273227975","2.675546611283106"]],"shownColumns":8,"totalColumns":53,"truncatedColumns":true},"tests/fixtures/covariate_hidden_factor/expected/Marchenko_PC.gz":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","0","1","0","1"],["age","67.06","82.92","87.76","64.57","81.62","66.44","75.53"],["PC1","-0.7904","-0.1993","0.3059","2.1952","-0.0345","-0.4571","0.7942"]],"shownColumns":8,"totalColumns":50,"truncatedColumns":true},"tests/fixtures/covariate_hidden_factor/expected/Buja_Eyuboglu_PC.gz":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","0","1","0","1"],["age","67.06","82.92","87.76","64.57","81.62","66.44","75.53"],["PC1","-0.7904","-0.1993","0.3059","2.1952","-0.0345","-0.4571","0.7942"]],"shownColumns":8,"totalColumns":50,"truncatedColumns":true},"tests/fixtures/covariate_hidden_factor/expected/PEER.factors.tsv":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["Factor1","-1.9689868302480802","-0.5777142629714919","-1.1097844168668152","-0.31776012143574744","0.9316883100761433","0.461826912428385","1.2043828829636531"],["Factor2","0.4928233935806234","-0.08549472177185433","0.8183972887349434","-0.9338565272256283","-0.6584489418683644","-0.4483268381001687","1.823597083931354"],["Factor3","0.3501340710245686","0.14571533939177014","-0.5173588766334256","-0.292175817326537","0.8664977538348799","1.1397705268157454","-0.10010811198261901"]],"shownColumns":8,"totalColumns":50,"truncatedColumns":true},"tests/fixtures/covariate_hidden_factor/expected/PEER.weights.tsv":{"kind":"table","rows":[["feature","Factor1","Factor2","Factor3","Factor4","Factor5"],["ENSG00000283047","-1.7436415740900164","0.2583746743255404","0.47822872128514793","0.5615754310448298","-0.9215818059252844"],["ENSG00000130538","-0.049466108478791494","0.38421328122758064","0.2847230657691795","-0.5102580319457181","0.45561780188119266"],["ENSG00000231565","-0.008886816628110559","-0.466616472403423","0.5875801940739112","-0.3895713470241593","0.15342578346522723"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/covariate_hidden_factor/expected/PEER.variance.tsv":{"kind":"table","rows":[["factor","r2"],["Factor1","3.361230579495944"],["Factor2","3.297627272191017"],["Factor3","2.536700993320218"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/covariate_hidden_factor/expected/PEER.gz":{"kind":"table","rows":[["#id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","0","1","0","1"],["age","67.06","82.92","87.76","64.57","81.62","66.44","75.53"],["PC1","-0.7904","-0.1993","0.3059","2.1952","-0.0345","-0.4571","0.7942"]],"shownColumns":8,"totalColumns":50,"truncatedColumns":true},"tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr1.tsv":{"kind":"table","rows":[["variant_id","gnomad_MAF"],["chr1:1000:C:G","0.14834847690550854"],["chr1:1037:A:T","0.4960064205828956"],["chr1:1074:A:G","0.12478507852411996"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/ems_training/protocol_example.gnomad_MAF_chr2.tsv":{"kind":"table","rows":[["variant_id","gnomad_MAF"],["chr2:1000:T:T","0.24893867622188837"],["chr2:1037:A:A","0.2905828566430643"],["chr2:1074:G:C","0.12085436431595521"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/ems_training/model_config.yaml":{"kind":"table","rows":[["#","Toy","model","configuration","for","EMS","training/prediction","MWE"],["system:"],["temp_directory:","\"/tmp/ems_dask\""],["random_seeds:"]],"shownColumns":8,"totalColumns":8,"truncatedColumns":false},"tests/fixtures/ems_training/expected/features_importance_model5_chr_chr2_NPR_1.csv":{"kind":"table","rows":[["feature","importance"],["chrombpnet_positive","25.262471700633572"],["tf_positive","14.94907294258858"],["gnomad_MAF","14.039430745796125"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/ems_training/expected/model_5_summary_chr_chr2_NPR_1.json":{"kind":"table","rows":[["{\"CatBoost\":{\"standard_subset_weighted\":{\"AP_test\":0.49887492","AUC_test:0.50612204","params:{\"iterations\":50","depth:4","learning_rate:0.1","loss_function:\"Logloss\"","random_seed:0","logging_level:\"Silent\""]],"shownColumns":8,"totalColumns":38,"truncatedColumns":true},"tests/fixtures/ems_training/expected/predictions_weighted_model_chr2.tsv":{"kind":"table","rows":[["variant_id","gene_id","CHR","BP","REF","ALT","SNP","pip"],["chr1:1000:C:G","ENSG00000100019","1","1000","C","G","chr1:1000:C:G","0.2817534630608156"],["chr1:1037:A:T","ENSG00000100035","1","1037","A","T","chr1:1037:A:T","0.68284686124174"],["chr1:1074:A:G","ENSG00000100036","1","1074","A","G","chr1:1074:A:G","0.24044852098155267"]],"shownColumns":8,"totalColumns":28,"truncatedColumns":true},"tests/fixtures/eoo_enrichment/protocol_example.eoo_baseline_annotation.tsv.gz":{"kind":"table","rows":[["chr","BP","ref","alt","rsid","maf","ANNO_baseline"],["1","10000654","A","C","rs1_0","0.3734","0"],["1","10100228","C","T","rs1_1","0.0602","0"],["1","10200604","T","A","rs1_2","0.0246","0"]],"shownColumns":7,"totalColumns":7,"truncatedColumns":false},"tests/fixtures/eoo_enrichment/protocol_example.eoo_significant_variants.tsv.gz":{"kind":"table","rows":[["chr","pos"],["1","100015157"],["1","1000291"],["1","100065691"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/eoo_enrichment/expected/enrichment_results.rds":{"kind":"rds","lines":["Object: list [length 10]"," Components: summary, OR_blockJacknife, Enrichment_blockJacknife, OR, Enrichment, OR_sd, Enrichment_sd, Enrichment_Z_scores, ...","$summary: data.frame [2 x 13]"," Annotation OR OR_SE OR_log2 OR_SE_log2 Enrichment"," maf maf 1 0 0 0 1"," ANNO_baseline ANNO_baseline 1 0 0 0 1","","$OR_blockJacknife: matrix/array [22 x 2]"," maf ANNO_baseline"," [1,] 1 1"," [2,] 1 1"," [3,] 1 1","","$Enrichment_blockJacknife: matrix/array [22 x 2]"," maf ANNO_baseline"," [1,] 1 1"," [2,] 1 1"," [3,] 1 1","","$OR: numeric [length 2]"," Values: c(maf = 0, ANNO_baseline = 0)","$Enrichment: numeric [length 2]"," Values: c(maf = 1, ANNO_baseline = 1)","$OR_sd: numeric [length 2]"," Values: c(0, 0)"]},"tests/fixtures/eoo_enrichment/expected/enrichment_results_summary.tsv.gz":{"kind":"table","rows":[["Annotation","OR","OR_SE","OR_log2","OR_SE_log2","Enrichment","Enrichment_SE","Enrichment_log2"],["maf","1","0","0","0","1","0","0"],["ANNO_baseline","1","0","0","0","1","0","0"]],"shownColumns":8,"totalColumns":13,"truncatedColumns":true},"tests/fixtures/gene_annotation/protocol_example.atac.tsv":{"kind":"table","rows":[["ID","S0561","S0321","S1177","S1098","S1252","S1170","S0634"],["C22P107555","2.65660494706228","2.96635134658411","2.28130807122782","1.98238696298197","2.32521464070871","3.3786450787504","3.25578026613787"],["C22P107557","2.80449305810594","3.56480978765153","2.8300407115426","3.42626771666669","2.79542295970582","3.20668973364495","3.29702988602781"],["C22P107559","3.62969398452243","3.54653724981745","3.46664752019843","3.68920172704657","3.43819373054703","3.14576639188727","3.2703678752323"]],"shownColumns":8,"totalColumns":11,"truncatedColumns":true},"tests/fixtures/gene_annotation/protocol_example.rnaseq.bed.gz":{"kind":"table","rows":[["gene_id","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","4.46908614068004","3.6324384389436","0","0.926449274182614","8.44864560635242","16.3456237133014","4.07740959667351"],["ENSG00000273342","0","19.892726241898","13.6287618206549","28.5428919916226","10.1099209273507","17.0947587639983","0"],["ENSG00000128274","28.6051391056338","18.1638378952795","0","0.282770008563753","0","0","0.961627662095183"]],"shownColumns":8,"totalColumns":61,"truncatedColumns":true},"tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","strand","SAMPLE_001","SAMPLE_002","SAMPLE_003"],["chr22","10939387","10961337","ENSG00000283047","-","37.0768403309204","0","5.5832744229102"],["chr22","15528191","15529138","ENSG00000130538","+","0","1.08358035439567","8.91397741376836"],["chr22","15611758","15613095","ENSG00000231565","-","5.97808406328782","0","2.63711285656005"]],"shownColumns":8,"totalColumns":65,"truncatedColumns":true},"tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.gene_list.tsv":{"kind":"table","rows":[["#chr","start","end","gene_id","strand","gene_name"],["chr22","19146992","19150291","ENSG00000063515","-","GSC2"],["chr22","46267960","46294007","ENSG00000075234","+","TTC38"],["chr22","46360833","46537619","ENSG00000075275","-","CELSR1"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.rnaseq.bed.region_list.txt":{"kind":"table","rows":[["#chr","start","end","ID","strand","path"],["chr22","10939387","10961337","ENSG00000283047","-","protocol_example.rnaseq.bed.bed.gz"],["chr22","15528191","15529138","ENSG00000130538","+","protocol_example.rnaseq.bed.bed.gz"],["chr22","15611758","15613095","ENSG00000231565","-","protocol_example.rnaseq.bed.bed.gz"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","gene_name","SAMPLE_001","SAMPLE_002","SAMPLE_003"],["chr22","17592135","17628748","ENSG00000131100_P36543","ENSG00000131100","-2.13239682163646","0.122048029453446","-0.978243368936795"],["chr22","17787648","18024560","ENSG00000243156_Q7RTP6","ENSG00000243156","-1.98683058179618","-2.381935629468","0.506516811334827"],["chr22","20707690","20859416","ENSG00000241973_P42356","ENSG00000241973","-2.53078001781622","1.810765636291","0.607220843471353"]],"shownColumns":8,"totalColumns":65,"truncatedColumns":true},"tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.gene_list.tsv":{"kind":"table","rows":[["#chr","start","end","gene_id","strand","gene_name"],["chr22","21759656","21867679","ENSG00000100030","-","MAPK1"],["chr22","38483437","38507659","ENSG00000100201","-","DDX17"],["chr22","50343303","50445089","ENSG00000100239","+","PPP6R2"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.protein.no_coord.region_list.txt":{"kind":"table","rows":[["#chr","start","end","ID","path"],["chr22","17592135","17628748","ENSG00000131100_P36543","protocol_example.protein.no_coord.bed.gz"],["chr22","17787648","18024560","ENSG00000243156_Q7RTP6","protocol_example.protein.no_coord.bed.gz"],["chr22","20707690","20859416","ENSG00000241973_P42356","protocol_example.protein.no_coord.bed.gz"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.atac.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","S0561","S0321","S1177","S1098"],["22","10662152","10664678","C22P107555","2.65660494706228","2.96635134658411","2.28130807122782","1.98238696298197"],["22","16094161","16096165","C22P107557","2.80449305810594","3.56480978765153","2.8300407115426","3.42626771666669"],["22","16110745","16113398","C22P107559","3.62969398452243","3.54653724981745","3.46664752019843","3.68920172704657"]],"shownColumns":8,"totalColumns":14,"truncatedColumns":true},"tests/fixtures/gene_annotation/expected/protocol_example.atac.region_list.txt":{"kind":"table","rows":[["#chr","start","end","ID","path"],["22","10662152","10664678","C22P107555","protocol_example.atac.bed.gz"],["22","16094161","16096165","C22P107557","protocol_example.atac.bed.gz"],["22","16110745","16113398","C22P107559","protocol_example.atac.bed.gz"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.intron_count.tsv.leafcutter.clusters_to_genes.txt":{"kind":"table","rows":[["clu","genes"],["22:clu_10_+","ENSG00000236052"],["22:clu_11_-","ENSG00000185264"],["22:clu_12_-","ENSG00000183765"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.phenotype.bed.formated.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","16675539","16675540","22:16671178:16671518:clu_27_-:ENSG00000189295","0.3150","0.7467","0.4984","0.0886"],["chr22","16675539","16675540","22:16671588:16673600:clu_27_-:ENSG00000189295","0.8687","0.8932","0.4067","0.9612"],["chr22","16675539","16675540","22:16673752:16675123:clu_27_-:ENSG00000189295","0.6683","0.9086","0.4975","0.4455"]],"shownColumns":8,"totalColumns":24,"truncatedColumns":true},"tests/fixtures/gene_annotation/expected/protocol_example.leafcutter.phenotype.bed.phenotype_group.txt":{"kind":"table","rows":[["ID","gene"],["22:16671178:16671518:clu_27_-:ENSG00000189295","ENSG00000189295"],["22:16671178:16671518:clu_27_-:ENSG00000259271","ENSG00000259271"],["22:16671588:16673600:clu_27_-:ENSG00000189295","ENSG00000189295"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/gene_annotation/expected/protocol_example.psichomics.phenotype.formated.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","15750824","15750825","SE_51_ENSG00000235992","0.8639","0.0875","0.6938","0.0321"],["chr22","15855242","15855243","SE_29_ENSG00000215270","0.4620","0.4195","0.6668","0.0903"],["chr22","16659627","16659628","SE_8_ENSG00000249263","0.3273","0.9916","0.5155","0.9725"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/gene_annotation/expected/protocol_example.psichomics.phenotype.phenotype_group.txt":{"kind":"table","rows":[["SE_51_ENSG00000235992","ENSG00000235992_SE"],["SE_29_ENSG00000215270","ENSG00000215270_SE"],["SE_8_ENSG00000249263","ENSG00000249263_SE"],["SE_26_ENSG00000259271","ENSG00000259271_SE"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/generalized_TADB/protocol_example.brain_TADs.txt":{"kind":"table","rows":[["chr22","10700000","12700000"],["chr22","10750000","12650000"],["chr22","13000000","15000000"],["chr22","15200000","17200000"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/generalized_TADB/protocol_example.gene_start_end.tsv":{"kind":"table","rows":[["","#chr","start","end","gene_id","gene_name"],["1","chr22","10736171","10736283","ENSG00000277248","U2"],["2","chr22","10939388","10961338","ENSG00000283047","FRG1FP"],["3","chr22","11066417","11068174","ENSG00000279973","CU104787.1"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/generalized_TADB/expected/generalized_TAD.tsv":{"kind":"table","rows":[["chr22","10700000","12700000"],["chr22","13000000","15000000"],["chr22","15200000","17200000"],["chr22","17500000","19500000"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/generalized_TADB/expected/generalized_TADB.tsv":{"kind":"table","rows":[["#chr","start","end","index"],["chr22","0","13000000","TADB1"],["chr22","12650000","15300000","TADB2"],["chr22","15000000","17500000","TADB3"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/generalized_TADB/expected/TADB_enhanced_cis.bed":{"kind":"table","rows":[["#chr","start","end","gene_id"],["chr22","0","13000000","ENSG00000226444"],["chr22","0","13000000","ENSG00000276871"],["chr22","0","13000000","ENSG00000277248"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/generalized_TADB/expected/extended_TADB.bed":{"kind":"table","rows":[["#chr","start","end","index"],["chr22","0","13626642","TADB_1"],["chr22","12650000","16304556","TADB_2"],["chr22","14273854","18558149","TADB_3"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/genotype_formatting/geno/chr21.bim":{"kind":"table","rows":[["21","chr21:5091891_A_G","0","5091891","G","A"],["21","chr21:5097593_CGTCCCTTCCCGAGGTTCCAGGCGGACGT_C","0","5097593","C","CGTCCCTTCCCGAGGTTCCAGGCGGACGT"],["21","chr21:5097593_CGTCCCTTCCCGAGGTTCCAGGCGGACGT_CGTCCCTTCCCGAGGTTCCAGGCGGACGTGTCCCTTCCCGAGGTTCCAGGCGGACGT","0","5097593","CGTCCCTTCCCGAGGTTCCAGGCGGACGTGTCCCTTCCCGAGGTTCCAGGCGGACGT","CGTCCCTTCCCGAGGTTCCAGGCGGACGT"],["21","chr21:5097593_CGTCCCTTCCCGAGGTTCCAGGCGGACGT_TGTCCCTTCCCGAGGTTCCAGGCGGACGT","0","5097593","TGTCCCTTCCCGAGGTTCCAGGCGGACGT","CGTCCCTTCCCGAGGTTCCAGGCGGACGT"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/genotype_formatting/expected/ld_by_region.float16.rds":{"kind":"rds","lines":["Object: list [length 2]"," Components: ld, variant_ids","$ld: matrix/array [75 x 75]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] NaN 0 0 0 0 0"," [2,] NaN 1 0 0 0 0"," [3,] NaN NaN NaN 0 0 0","","$variant_ids: character [length 75]"," Values: c(\"chr22:16051446_C_A\", \"chr22:16054534_GCAAAGTGATC_G\", \"chr22:16054534_GCAAAGTGATC_TCAAAGTGATC\", \"chr22:16054540_T_*\", \"chr22:16054540_T_C\", \"chr22:16059969_T_A\" ) ..."]},"tests/fixtures/genotype_formatting/expected/plink_to_vcf.variants.tsv":{"kind":"table","rows":[["chr22","10526333","chr22:10526333_CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT_*","CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT","*"],["chr22","10526566","chr22:10526566_AC_*","AC","*"],["chr22","10657618","chr22:10657618_C_G","C","G"],["chr22","10684490","chr22:10684490_G_A","G","A"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/genotype_formatting/expected/vcf_to_plink.bim":{"kind":"table","rows":[["22","chr22:10526333_CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT_*","0","10526333","*","CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT"],["22","chr22:10526566_AC_*","0","10526566","*","AC"],["22","chr22:10657618_C_G","0","10657618","G","C"],["22","chr22:10684490_G_A","0","10684490","A","G"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/genotype_formatting/expected/genotype_by_region.bim":{"kind":"table","rows":[["chr22","chr22:16022590_G_T","0","16022590","T","G"],["chr22","chr22:16022788_G_T","0","16022788","T","G"],["chr22","chr22:16024185_G_A","0","16024185","A","G"],["chr22","chr22:16025239_GACAA_G","0","16025239","G","GACAA"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/genotype_formatting/expected/genotype_by_chrom.bim":{"kind":"table","rows":[["22","chr22:10526333_CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT_*","0","10526333","*","CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT"],["22","chr22:10526566_AC_*","0","10526566","*","AC"],["22","chr22:10657618_C_G","0","10657618","G","C"],["22","chr22:10684490_G_A","0","10684490","A","G"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/gregor/index.snps.txt":{"kind":"table","rows":[["22:19449483"],["22:41441787"],["22:39507863"],["22:29485708"]],"shownColumns":1,"totalColumns":1,"truncatedColumns":false},"tests/fixtures/gregor/test_peaks.bed":{"kind":"table","rows":[["chr22","19449433","19449533","."],["chr22","29485658","29485758","."]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/gregor/example_enrichment_results.txt":{"kind":"table","rows":[["Bed_File","InBed_Index_SNP","ExpectNum_of_InBed_SNP","PValue","N1_N2","Np","Np_Nn","odds"],["test_peaks.bed","1","0.4","0.880024175924493","2","4","30","7.35976894209104"],["other_peaks.bed","3","1.2","0.5","6","30","90","2.10"]],"shownColumns":8,"totalColumns":11,"truncatedColumns":true},"tests/fixtures/gregor/expected/enrichment_results.txt":{"kind":"table","rows":[["Bed_File","InBed_Index_SNP","ExpectNum_of_InBed_SNP","PValue","N1_N2","Np","Np_Nn","odds"],["test_peaks.bed","1","0.4","0.880024175924493","2","4","30","7.35976894209104"]],"shownColumns":8,"totalColumns":11,"truncatedColumns":true},"tests/fixtures/gsea/protocol_example.pathway_genes.tsv":{"kind":"table","rows":[["group","gene_id"],["geneset1","ENSG00000141510"],["geneset1","ENSG00000139618"],["geneset1","ENSG00000012048"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/gsea/expected/pathway_go_results.rds":{"kind":"rds","lines":["Object: data.frame [2706 x 17]"," category subcategory ID"," 1 Gene Ontology Biological Process GO:0000075"," 2 Gene Ontology Biological Process GO:0000077"," 3 Gene Ontology Biological Process GO:0000082"," Description GeneRatio BgRatio"," 1 cell cycle checkpoint signaling 3/10 187/18860"," 2 DNA damage checkpoint signaling 3/10 117/18860"," 3 G1/S transition of mitotic cell cycle 3/10 246/18860"]},"tests/fixtures/intact/README.md":{"kind":"table","rows":[["# INTACT integration fixture"],["Tiny hand-authored inputs for the `intact` step of"],["`code/SoS/pecotmr_integration/intact.ipynb`"," which joins PTWAS + fastenloc output"],["and runs the Bioconductor **INTACT** package."]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/intact/protocol_example.ptwas.output":{"kind":"table","rows":[["GENE","STAT","SUBCLASS"],["ENSG00000128272","6.8","0"],["ENSG00000100060","5.9","0"],["ENSG00000100075","-0.8","0"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/intact/expected/intact.rds":{"kind":"rds","lines":["Object: data.frame [5 x 5]"," gene zscore GLCP intact_pip fdr_sig"," 1 ENSG00000128272 6.8 0.95 1.0000000 TRUE"," 2 ENSG00000100060 5.9 0.90 0.9999992 TRUE"," 3 ENSG00000183765 2.1 0.22 0.2599521 FALSE"]},"tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.bim":{"kind":"table","rows":[["22","chr22:10526333_CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT_*","0","10526333","*","CGCCGCCGCGGGTTTTTTCCCCCGCCGCCGCGGCTTTTTGTGTTTTTTTGCCCCCGATGCTTTCGGCCCCCGCCGCCGCAGCGGCTTTTTGCCCCCGCCCCCAACACCGCGGATTTTTCTCCCCGACGCCGCGGCTTTTTGCCGCCGCCGCCACCGGCACGGCTTTTTGGCCGCGGCGACTTTTTGCGCCCACCGCGGCGGCTTTTTGCTCCCCGCCGCCGCGGTTTTTGCCAACGCGGCTTTTTACCCCCCTCGCCGCGGCTTTT"],["22","chr22:10526566_AC_*","0","10526566","*","AC"],["22","chr22:10657618_C_G","0","10657618","G","C"],["22","chr22:10684490_G_A","0","10684490","A","G"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/ld_prune_reference/genotype/protocol_example.ld_genotype.chr22.fam":{"kind":"table","rows":[["0","SAMPLE_001","0","0","0","-9"],["0","SAMPLE_002","0","0","0","-9"],["0","SAMPLE_003","0","0","0","-9"],["0","SAMPLE_004","0","0","0","-9"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/mash/mashr_input.rds":{"kind":"rds","lines":["Object: list [length 9]"," Components: strong.b, strong.s, random.b, random.s, null.b, null.s, strong.z, random.z, ...","$strong.b: matrix/array [17 x 8]"," ALL Ast End Exc Inh Mic"," [1,] 0.2490760 0.1114970 -0.0011690 0.2058550 0.202667 0.1912040"," [2,] 0.0927035 -0.0548178 -0.0848382 -0.0164813 0.152236 0.2678570"," [3,] 0.3317760 -0.0481282 0.0288251 0.3373930 0.235520 0.0615115","","$strong.s: matrix/array [17 x 8]"," ALL Ast End Exc Inh Mic"," [1,] 0.0284034 0.0527114 0.0835386 0.0265783 0.0505712 0.0577236"," [2,] 0.0797889 0.1836720 0.3142610 0.0785934 0.1371430 0.2012280"," [3,] 0.0362086 0.0708372 0.1085490 0.0344021 0.0442136 0.0717070","","$random.b: matrix/array [50 x 8]"," ALL Ast End Exc Inh Mic"," [1,] -0.00798796 -0.0162711 0.0247252 0.000681081 0.0151881 0.02678640"," [2,] 0.02479720 -0.0164770 -0.2460290 -0.003475240 0.1236060 0.00559492"," [3,] 0.03869450 -0.0110320 0.0153863 0.027399300 -0.0412417 0.01414480","","$random.s: matrix/array [50 x 8]"," ALL Ast End Exc Inh Mic"," [1,] 0.0279764 0.0492038 0.0747612 0.0262017 0.0485652 0.0519510"," [2,] 0.0272888 0.0476498 0.0744156 0.0247977 0.0451990 0.0510565"," [3,] 0.0284164 0.0513249 0.0815680 0.0261559 0.0472089 0.0559238","","$null.b: matrix/array [50 x 8]"," ALL Ast End Exc Inh Mic"," [1,] -0.0379178 0.1762690 0.2869070 -0.00898611 -0.0313426 -0.14192800"," [2,] -0.0283940 -0.0179526 -0.0189619 0.00314473 -0.0381750 -0.00009733"," [3,] -0.0339721 -0.0189439 -0.1838430 0.09053870 -0.2164520 -0.04149890","","$null.s: matrix/array [50 x 8]"," ALL Ast End Exc Inh Mic"," [1,] 0.0745909 0.1287650 0.2205520 0.0691947 0.125623 0.1375720"," [2,] 0.0247090 0.0434852 0.0680688 0.0228944 0.042475 0.0481976"," [3,] 0.0804790 0.1346920 0.2214130 0.0735394 0.137780 0.1484620"]},"tests/fixtures/mash/region_strong.rds":{"kind":"rds","lines":["Object: list [length 2]"," Components: bhat, sbhat","$bhat: matrix/array [17 x 8]"," ALL Ast End Exc Inh Mic"," [1,] 0.2490760 0.1114970 -0.0011690 0.2058550 0.202667 0.1912040"," [2,] 0.0927035 -0.0548178 -0.0848382 -0.0164813 0.152236 0.2678570"," [3,] 0.3317760 -0.0481282 0.0288251 0.3373930 0.235520 0.0615115","","$sbhat: matrix/array [17 x 8]"," ALL Ast End Exc Inh Mic"," [1,] 0.0284034 0.0527114 0.0835386 0.0265783 0.0505712 0.0577236"," [2,] 0.0797889 0.1836720 0.3142610 0.0785934 0.1371430 0.2012280"," [3,] 0.0362086 0.0708372 0.1085490 0.0344021 0.0442136 0.0717070"]},"tests/fixtures/mash/Ast_De_Jager_eQTL.tsv":{"kind":"table","rows":[["variant_id","z","pip","cs_95"],["chr22:15528227:A:G","0.980877384590622","0.88470232298132","1"],["chr22:15528295:A:G","0.0285784073543268","0.0310205016518012","1"],["chr22:15528301:A:G","-2.77425597107817","0.00847883833339438","0"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/mash/expected/mash_model.EE.rds":{"kind":"rds","lines":["Object: list [length 3]"," Components: mash_model, vhat_file, prior_file","$mash_model: mash [length 9]"," Components: result, loglik, vloglik, null_loglik, alt_loglik, fitted_g, posterior_weights, alpha, ...","$vhat_file: character [length 1]"," Values: \"vhat.rds\"","$prior_file: character [length 1]"," Values: \"prior.rds\""]},"tests/fixtures/mash_posterior/orig.rds":{"kind":"rds","lines":["Object: list [length 2]"," Components: bhat, sbhat","$bhat: matrix/array [17 x 8]"," ALL Ast End Exc Inh Mic"," mash::mash::var1 0.2490760 0.1114970 -0.0011690 0.2058550 0.202667 0.1912040"," mash::mash::var2 0.0927035 -0.0548178 -0.0848382 -0.0164813 0.152236 0.2678570"," mash::mash::var3 0.3317760 -0.0481282 0.0288251 0.3373930 0.235520 0.0615115","","$sbhat: matrix/array [17 x 8]"," ALL Ast End Exc Inh Mic"," mash::mash::var1 0.0284034 0.0527114 0.0835386 0.0265783 0.0505712 0.0577236"," mash::mash::var2 0.0797889 0.1836720 0.3142610 0.0785934 0.1371430 0.2012280"," mash::mash::var3 0.0362086 0.0708372 0.1085490 0.0344021 0.0442136 0.0717070"]},"tests/fixtures/mash_posterior/posterior.rds":{"kind":"rds","lines":["Object: list [length 2]"," Components: PosteriorMean, PosteriorCov","$PosteriorMean: matrix/array [17 x 8]"," ALL Ast End Exc Inh"," mash::mash::var1 0.17232694 0.17232694 0.1723269 0.17232694 0.17232694"," mash::mash::var2 0.01476307 0.01371301 0.0138452 0.01396853 0.01452357"," mash::mash::var3 0.19616044 0.19612898 0.1961331 0.19616209 0.19614862"," Mic"," mash::mash::var1 0.17232694"," mash::mash::var2 0.01446077"," mash::mash::var3 0.19613361","","$PosteriorCov: array [8 x 8 x 17]"," Values: structure(c(0.000202672673211838, 0.000202672660415168, 0.000202672657334736, 0.000202672667085849, 0.000202672663157249, 0.00020267266205673, 0.000202672660415168, 0.000202672795588284, 0.000202672833044135, 0.000202672685212499, 0.000202672744772269, 0.000202672761456718, 0.000202672657334736, 0.000202672833044135, 0.000202672931435478, 0.000202672691934771, 0.000202672775039266, 0.00020267279831929, 0.000202672667085849, 0.000202672685212499, 0.000202672691934771, 0.000202672674726484, 0.000202672679228567, 0.000202672681630198, 0.000202672663157249, 0.000202672744772269, 0.000202672775039266, 0.000202672679228567, 0.000202672726740776, 0.00020267272864298, 0.00020267266205673, 0.000202672761456718, 0.00020267279831929, 0.000202672681630198, 0.00020267272864298, 0.000202672751774356, 0.00020267265981273, 0.000202672795476713, 0.000202672845787816, 0.000202672686527169, 0.000202672750691565, 0.000202672768665906, 0.000202672661847772, 0.000202672764624715, 0.000202672802739626, 0.000202672682086218, 0.000202672730696178, 0.000202672744313261, 0.000690993805157277, 0.00064588947618887, 0.000640967943391216, 0.000641530067803991, 0.000643924292552219, 0.000643674331326419, 0.000645889476188869, 0.000906337969893488, 0.000660843769945103, 0.000658827651347361, 0.000649775937341229, 0.000650796801674549, 0.000640967943391216, 0.000660843769945103, 0.000946162423800497, 0.000657521735095652, 0.000645922237620323, 0.000647225958350737, 0.00064153006780399, 0.000658827651347361, 0.000657521735095652, 0.00070123653112158, 0.000645684987210976, 0.000646776497020376, 0.000643924292552219, 0.000649775937341229, 0.000645922237620323, 0.000645684987210976, 0.000697969329821666, 0.000644665087109268, 0.000643674331326419, 0.000650796801674549, 0.000647225958350737, 0.000646776497020376, 0.000644665087109268, 0.000700828034552002, 0.000643720389557597, 0.000658795526524022, 0.000657038767921531, 0.000655247701009095, 0.000647192071802993, 0.000648102814940983, 0.000647339097446576, 0.000637165970042156, 0.000629745191532584, 0.000632198400689406, 0.000642953957670517, 0.000641780977968221, 0.000274996475008921, 0.000274597826351489, 0.000274634478875012, 0.000274895102245494, 0.000274774091543306, 0.000274639389100835, 0.000274597826351489, 0.000281431493974582, 0.000280358572781969, 0.000274250357578359, 0.00027708647863036, 0.000280243492112642, 0.000274634478875012, 0.000280358572781969, 0.000280445768474198, 0.000274334023718417, 0.000276786408681874, 0.000279516268320755, 0.000274895102245494, 0.000274250357578359, 0.000274334023718417, 0.000275037883252331, 0.000274652715367439, 0.000274345232213175, 0.000274774091543306, 0.00027708647863036, 0.000276786408681874, 0.000274652715367439, 0.000275789325082154, 0.000276746209238406, 0.000274639389100835, 0.000280243492112642, 0.000279516268320755, 0.000274345232213175, 0.000276746209238406, 0.000279634287359727, 0.000274663578648915, 0.00027967656307664, 0.000279026046564802, 0.000274400449314018, 0.000276548172226491, 0.000278938898877881, 0.00027466945735434, 0.000279538784187142, 0.000278906909591904, 0.000274413868543016, 0.000276500043945783, 0.000278822259304957, 0.000243281632388456, 0.000241795439336516, 0.000241797415180052, 0.000241833578726501, 0.000241815300590824, 0.000241798139468473, 0.000241795439336516, 0.000256479144466209, 0.000251769476880683, 0.000240547077465417, 0.000248787965574156, 0.000252553632148097, 0.000241797415180052, 0.000251769476880683, 0.000260489774022465, 0.000240717005884792, 0.000247849295923747, 0.000251108160206683, 0.000241833578726501, 0.000240547077465417, 0.000240717005884792, 0.000243360339092181, 0.000241059665886509, 0.000240632833846987, 0.000241815300590824, 0.000248787965574156, 0.000247849295923747, 0.000241059665886509, 0.000249068840998951, 0.000248325810003554, 0.000241798139468473, 0.000252553632148097, 0.000251108160206683, 0.000240632833846987, 0.000248325810003554, 0.000254747379551046, 0.000241759272162351, 0.000261187793242159, 0.000258580305127097, 0.000239654693045589, 0.000253542422229809, 0.000259898858496253, 0.000241770756568511, 0.000258761083419835, 0.000256480205151462, 0.00023993022266498, 0.000252076606781728, 0.00025763399641408, 0.0012162150643112, 0.00105841475958492, 0.00099789215580201, 0.00109717070864458, 0.00111027302309506, 0.0011059306632207, 0.00105841475958492, 0.00201090514963266, 0.000890520831266493, 0.00105329284087923, 0.00107480446181259, 0.00106765526207329, 0.000997892155802011, 0.000890520831266493, 0.00272846838468087, 0.0010322026880077, 0.000888460328375229, 0.000936540132388815, 0.00109717070864458, 0.00105329284087923, 0.0010322026880077, 0.00121223562590308, 0.00110349561706699, 0.0011007606837934, 0.00111027302309506, 0.00107480446181259, 0.000888460328375229, 0.00110349561706699, 0.00125554273052434, 0.00112246960708966, 0.0011059306632207, 0.00106765526207329, 0.000936540132388814, 0.0011007606837934, 0.00112246960708966, 0.00124046302930025, 0.00110760396025058, 0.0010713326286195, 0.000897965557158104, 0.00110119992489324, 0.00112808001069332, 0.00111913263565441, 0.00110491159726185, 0.00106597969328927, 0.000947774459845704, 0.00110011731781844, 0.00112025190406249, 0.0011135595100208, 1.51088082811018e-15, 2.19984553031266e-16, -5.78963271964974e-16, 2.0703314394745e-15, -2.32589281542517e-16, -2.98227992799423e-16, 2.19984553031266e-16, 9.61326857415861e-16, -1.7433689389371e-16, 6.27067958414194e-16, -6.95634016799429e-17, -8.94146069778939e-17, -5.78963271964974e-16, -1.7433689389371e-16, 4.59375528933787e-15, -1.65795697336437e-15, 1.88540698345908e-16, 2.41172166792823e-16, 2.0703314394745e-15, 6.27067958414194e-16, -1.65795697336437e-15, 6.83010794287169e-15, -6.67330523084712e-16, -8.55017243819948e-16, -2.32589281542517e-16, -6.95634016799429e-17, 1.88540698345908e-16, -6.67330523084712e-16, 8.82644412311252e-16, 9.78472912801509e-17, -2.98227992799423e-16, -8.94146069778939e-17, 2.41172166792823e-16, -8.55017243819948e-16, 9.78472912801509e-17, 7.82554651622793e-16, 2.0010586931819e-14, 6.03269805938047e-15, -1.60953414520564e-14, 5.72547248121967e-14, -6.5003962690404e-15, -8.32350742726878e-15, -1.51655128732836e-15, -4.57968342961883e-16, 1.21802700153181e-15, -4.33970693474545e-15, 4.9143712845081e-16, 6.29089812368518e-16, 1.08617619551487e-08, -3.9242918512654e-08, -2.8140172440362e-09, -1.57148994844309e-09, 3.16743399688553e-09, 1.11659687239979e-09, -3.9242918512654e-08, 0.00187489135683699, 1.15992321848839e-08, 6.47763140550062e-09, -1.30560672686515e-08, -4.60255583328996e-09, -2.8140172440362e-09, 1.15992321848839e-08, 1.55872817287606e-08, 4.64561534001302e-10, -9.36199917985853e-10, -3.30000706958992e-10, -1.57148994844309e-09, 6.47763140550062e-09, 4.64561534001302e-10, 1.75677385239271e-09, -5.22808409550424e-10, -1.84272727373226e-10, 3.16743399688553e-09, -1.30560672686515e-08, -9.36199917985853e-10, -5.22808409550424e-10, 4.60243376260227e-09, 3.71521422032048e-10, 1.11659687239979e-09, -4.60255583328996e-09, -3.30000706958992e-10, -1.84272727373226e-10, 3.71521422032048e-10, 6.55629183612458e-09, 1.8754261763856e-08, -7.73031094264582e-08, -5.54347406681391e-09, -3.09575799861647e-09, 6.23962311533508e-09, 2.19960982426364e-09, 1.7371432908383e-08, -7.16039279072896e-08, -5.13471720318283e-09, -2.86749094167462e-09, 5.77953554784623e-09, 2.03741514625023e-09, 0.000204507192785026, 3.96218053641124e-05, 1.0638090174294e-05, 1.61065860410035e-06, 6.08076132387482e-06, -4.62878478097471e-06, 3.96218053641124e-05, 0.00234308748966294, 0.000470020596846252, 7.11625828239816e-05, 0.000268663608247443, -0.000204511934881824, 1.0638090174294e-05, 0.000470020596846252, 0.00347589952822904, 1.91064920134712e-05, 7.21338005448661e-05, -5.49096706033319e-05, 1.61065860410035e-06, 7.11625828239816e-05, 1.91064920134712e-05, 0.000162208803157109, 1.0921332417337e-05, -8.31351204282455e-06, 6.08076132387482e-06, 0.000268663608247443, 7.21338005448661e-05, 1.0921332417337e-05, 0.000426405075762334, -3.13863780413286e-05, -4.62878478097471e-06, -0.000204511934881824, -5.49096706033319e-05, -8.31351204282455e-06, -3.13863780413286e-05, 0.000484340050623577, -6.40371054829753e-05, -0.00302315031152417, -0.000759618231467465, -0.000115014225811381, -0.000434207463850975, 0.000330524580872117, 6.59305846579617e-06, 0.000291302007193957, 7.82122829802096e-05, 1.18414170438043e-05, 4.47058211420251e-05, -3.40310103200913e-05, 0.000595627591790756, -1.98350763981961e-11, 3.91331324983701e-11, 3.09154657169436e-11, -1.85910286297497e-10, 4.14389647596103e-10, -1.98350763981961e-11, 0.00101876178563553, -8.68173176578335e-12, -6.85862922445574e-12, 4.12444804871737e-11, -9.19329430290605e-11, 3.91331324983701e-11, -8.68173176578335e-12, 0.00286690437068185, 1.35315878510914e-11, -8.13722218946655e-11, 1.81376779914699e-10, 3.09154657169436e-11, -6.85862922445574e-12, 1.35315878510914e-11, 0.000719564739496544, -6.42846544225695e-11, 1.43288999589208e-10, -1.85910286297497e-10, 4.12444804871737e-11, -8.13722218946655e-11, -6.42846544225695e-11, 0.00125167506309381, -8.61669211676963e-10, 4.14389647596103e-10, -9.19329430290605e-11, 1.81376779914699e-10, 1.43288999589208e-10, -8.61669211676963e-10, 0.000818895666242797, 6.81933854003447e-11, -1.51287890093159e-11, 2.98479919166178e-11, 2.35801376254757e-11, -1.41799223404848e-10, 3.16067141209464e-10, -1.3300845938969e-11, 2.95082481940965e-12, -5.82172407070231e-12, -4.59920204134642e-12, 2.76574001331284e-11, -6.16476633196611e-11, 0.000382188647098703, 9.20133193457273e-05, 0.000254400144161898, 0.000219767233912923, 0.000118171478661359, -0.000102338231280768, 9.20133193457273e-05, 0.000511500084436223, 8.04048954642997e-05, 8.45954491926936e-05, 9.68651898501585e-05, 0.000123516784705527, 0.000254400144161898, 8.04048954642997e-05, 0.00188017700353292, 0.00041533734802655, 0.000149139757186764, -0.0004294190307933, 0.000219767233912923, 8.45954491926936e-05, 0.00041533734802655, 0.000561433953395943, 0.000137923370189886, -0.00031102686876138, 0.000118171478661359, 9.68651898501585e-05, 0.000149139757186764, 0.000137923370189886, 0.000372837421428478, 3.41404996661138e-05, -0.000102338231280768, 0.000123516784705527, -0.0004294190307933, -0.00031102686876138, 3.41404996661138e-05, 0.00107380670893907, 0.000142016132344844, 0.000103321680113364, 0.000189064968920016, 0.000173700683259049, 0.000121189940378943, 1.38025891907582e-05, 8.87214762321567e-05, 0.000100424332953944, 7.18818694145038e-05, 7.79607181979821e-05, 9.57598660555519e-05, 0.000134421602409216, 0.000178283467503444, 0.000178278184073295, 0.000178276921940647, 0.000178282130042361, 0.000178279652493857, 0.000178277628716052, 0.000178278184073292, 0.000178311419270022, 0.000178318092984915, 0.000178281202824926, 0.000178298751865903, 0.000178313086737932, 0.000178276921940647, 0.000178318092984919, 0.000178336399506422, 0.000178280935159633, 0.000178304265381162, 0.000178323322590716, 0.000178282130042361, 0.000178281202824929, 0.000178280935159633, 0.000178283037822448, 0.000178281514238363, 0.000178281085048287, 0.000178279652493857, 0.000178298751865907, 0.000178304265381162, 0.000178281514238363, 0.000178294510846229, 0.000178301177895732, 0.000178277628716049, 0.000178313086737932, 0.000178323322590712, 0.000178281085048283, 0.000178301177895728, 0.000178320242015004, 0.000178277956737857, 0.000178310763286595, 0.000178320233724643, 0.000178281154613158, 0.000178299744961592, 0.000178314930421964, 0.000178277288880306, 0.00017831549387029, 0.000178326522704823, 0.00017828101297802, 0.000178302662438189, 0.000178320346723538, 0.000249255745722262, 1.40880624365891e-07, 1.9715500381946e-06, 1.44137714799125e-06, 3.07396479046597e-07, -4.51303962743701e-07, 1.40880624365891e-07, 0.00100342264674554, 1.42830751626548e-07, 1.0442104419827e-07, 2.22705038258351e-08, -3.26936348327063e-08, 1.9715500381946e-06, 1.42830751626548e-07, 0.00343307096443373, 1.46131897195423e-06, 3.11650344277689e-07, -4.57546769215339e-07, 1.44137714799125e-06, 1.0442104419827e-07, 1.46131897195423e-06, 0.000186512634321463, 2.27843126195592e-07, -3.34508047380045e-07, 3.07396479046597e-07, 2.22705038258351e-08, 3.11650344277689e-07, 2.27843126195592e-07, 0.000435506111955378, -7.13379201916996e-08, -4.51303962743701e-07, -3.26936348327063e-08, -4.57546769215339e-07, -3.34508047380045e-07, -7.13379201916996e-08, 0.00032656550202865, -1.45302778015036e-06, -1.05264256453213e-07, -1.473130071733e-06, -1.07698884906256e-06, -2.2968401122719e-07, 3.37212811064879e-07, 5.76881743374023e-07, 4.17935999858247e-08, 5.848641420848e-07, 4.27586436223693e-07, 9.11906872839524e-08, -1.33878629372092e-07, 0.000476168992138329, 1.95505236676857e-07, -1.96494067727059e-05, 1.6705981921647e-06, -5.90413303049736e-07, -2.73361238952233e-05, 1.95505236676857e-07, 0.00126654506228381, 5.61397091835593e-06, 6.97193737200785e-07, 1.22325348208586e-06, 7.37514675118629e-06, -1.96494067727059e-05, 5.61397091835593e-06, 0.00295317232758473, -4.61556787708425e-06, 1.1009786747453e-05, 0.00019559360022598, 1.6705981921647e-06, 6.97193737200785e-07, -4.61556787708425e-06, 0.000448459216604951, 4.84351901636551e-07, -6.67539108392332e-06, -5.90413303049736e-07, 1.22325348208586e-06, 1.1009786747453e-05, 4.84351901636551e-07, 0.000700663822569031, 1.47952436041175e-05, -2.73361238952233e-05, 7.37514675118629e-06, 0.00019559360022598, -6.67539108392332e-06, 1.47952436041175e-05, 0.00170799025564566, -1.31961287402264e-05, 4.12788685931432e-06, 9.80254410011738e-05, -2.88857963325778e-06, 7.82563767859671e-06, 0.000134378719960182, -1.3412966566235e-05, 4.17740510953442e-06, 9.95206733654617e-05, -2.94673627831521e-06, 7.93229002180084e-06, 0.000136433836552945, 0.000421979198726787, 1.13502443441796e-07, 4.73534292340979e-05, 6.65643627620295e-06, 4.90204982843e-06, -2.02431411253556e-06, 1.13502443441796e-07, 0.000583822495446347, -4.37931355281077e-05, -3.15894819838565e-06, 1.98956308238779e-06, 7.8354283101314e-06, 4.73534292340979e-05, -4.37931355281077e-05, 0.00436803302215065, 8.874997682797e-05, 3.7633586527917e-05, -7.32476741814054e-05, 6.65643627620295e-06, -3.15894819838565e-06, 8.874997682797e-05, 0.000409007711222281, 5.99510303218647e-06, -6.69934497095283e-06, 4.90204982843e-06, 1.98956308238779e-06, 3.7633586527917e-05, 5.99510303218647e-06, 0.000788317036838579, -1.71343463960651e-08, -2.02431411253556e-06, 7.8354283101314e-06, -7.32476741814054e-05, -6.69934497095283e-06, -1.71343463960651e-08, 0.0015250353968028, -2.1029179037886e-06, 8.30095299928014e-06, -7.70150021644302e-05, -7.04191064868456e-06, 4.39369919681448e-08, 1.06712685958719e-05, -3.47654986650815e-06, 8.89687070067821e-06, -9.54645533167561e-05, -9.27926214133528e-06, -1.2690706909683e-06, 1.20464648574159e-05, 0.000249756437369473, -8.33416335239631e-06, -3.44846565495686e-05, 1.58719291516668e-05, -1.86246542184531e-05, -1.56169034648021e-05, -8.33416335239631e-06, 0.00067735104886479, 0.000106509506671276, -2.79267269894539e-05, 7.41822929238144e-05, 6.09868079386546e-05, -3.44846565495686e-05, 0.000106509506671276, 0.00347343098442299, -7.83200055332438e-05, 0.000166466175699259, 0.000137868705430516, 1.58719291516668e-05, -2.79267269894539e-05, -7.83200055332438e-05, 0.000247760262522392, -4.81381140309172e-05, -3.98839091053278e-05, -1.86246542184531e-05, 7.41822929238144e-05, 0.000166466175699259, -4.81381140309172e-05, 0.000673005297244339, 9.23529330054558e-05, -1.56169034648021e-05, 6.09868079386546e-05, 0.000137868705430516, -3.98839091053278e-05, 9.23529330054558e-05, 0.00120726744934011, 1.62010213605479e-05, 1.17498258067481e-05, -1.19548487142989e-05, 1.5072691198294e-05, 3.11897863126704e-06, 1.34860040425797e-06, 1.35143196403646e-05, 1.10354442924136e-05, -7.53743234578001e-06, 1.21771407382868e-05, 4.32781586171102e-06, 2.58765789546014e-06, 5.84723353744217e-07, 5.66806597235321e-08, 5.45331376396812e-07, 2.84740219364165e-07, 2.16192206508e-07, 1.7487190102632e-07, 5.66806597235322e-08, 9.39636853520967e-07, -3.06560512281921e-07, 3.50208990017659e-08, 1.24202054663647e-07, 1.78413240768835e-07, 5.45331376396812e-07, -3.06560512281921e-07, 3.93454533297325e-06, 6.12070253157238e-07, 3.36985293286573e-07, 1.70220888475508e-07, 2.84740219364165e-07, 3.5020899001766e-08, 6.12070253157238e-07, 6.2259506502226e-07, 2.23391714417547e-07, 1.74595492236862e-07, 2.16192206508e-07, 1.24202054663646e-07, 3.36985293286573e-07, 2.23391714417547e-07, 6.91087192409985e-07, 1.75730311876578e-07, 1.7487190102632e-07, 1.78413240768835e-07, 1.70220888475508e-07, 1.74595492236862e-07, 1.75730311876578e-07, 8.17309705480943e-07, 3.62133562176226e-06, -2.13900739036425e-06, 1.04681674151376e-05, 4.03614796482439e-06, 2.30523689546651e-06, 1.28818395167377e-06, 3.20419085590143e-07, -1.23422694318489e-08, 7.57219890809184e-07, 3.46473982779527e-07, 2.39165398790199e-07, 1.73982425325082e-07, 0.000815425697065525, 0.000322983302059327, 0.000355803024467498, 0.000271459055634256, 0.000304269733382108, 0.00027499145557414, 0.000322983302059327, 0.00977568015145744, 0.0099610360454617, 0.00655251076072851, 0.00787846287951198, 0.00669526284240114, 0.000355803024467498, 0.0099610360454617, 0.017934130512115, 0.00755478832393643, 0.00908708912978019, 0.00771975591706234, 0.000271459055634256, 0.00655251076072851, 0.00755478832393643, 0.00636790267383328, 0.00598101961309056, 0.00508689343582039, 0.000304269733382108, 0.00787846287951198, 0.00908708912978019, 0.00598101961309056, 0.0085694021122118, 0.00611110457710638, 0.00027499145557414, 0.00669526284240114, 0.00771975591706234, 0.00508689343582039, 0.00611110457710638, 0.00659351995538288, 0.000267097385890687, 0.0063762465394884, 0.00735109333332331, 0.00484581768852353, 0.00582039621050936, 0.00495074086866018, 4.46556985217172e-05, -0.00261310530646169, -0.00303720863701038, -0.00194729814154248, -0.00237128478695276, -0.00199294456741381 ), dim = c(6L, 8L, 17L), dimnames = list(c(\"ALL\", \"Ast\", \"End\", \"Exc\", \"Inh\", \"Mic\"), c(\"ALL\", \"Ast\", \"End\", \"Exc\", \"Inh\", \"Mic\", \"OPC\", \"Oli\"), c(\"mash::mash::var1\", \"mash::mash::var2\", \"mash::mash::var3\", \"mash::mash::var4\", \"mash::mash::var5\", \"mash::mash::var6\", \"mash::mash::var7\", \"mash::mash::var8\", \"mash::mash::var9\", \"mash::mash::var10\", \"mash::mash::var11\", \"mash::mash::var12\", \"mash::mash::var13\", \"mash::mash::var14\", \"mash::mash::var15\", \"mash::mash::var16\", \"mash::mash::var17\"))) ..."]},"tests/fixtures/mash_posterior/fine_mapping.rds":{"kind":"rds","lines":["Object: data.frame [17 x 3]"," variants cs_order pip"," 1 mash::mash::var1 1 0.60"," 2 mash::mash::var2 1 0.40"," 3 mash::mash::var3 0 0.02"]},"tests/fixtures/mash/expected/mash_input.qss.rds":{"kind":"rds","lines":["Object: list [length 10]"," Components: strong.b, strong.s, random.b, random.s, null.b, null.s, random.z, null.z, ...","$strong.b: matrix/array [2 x 2]"," Mic_De_Jager_eQTL"," protocol_example::mash::chr22:15528675:A:G_region1.qss 3.0964631"," protocol_example::mash::chr22:15528699:A:G_region1.qss 0.3039547"," Ast_De_Jager_eQTL"," protocol_example::mash::chr22:15528675:A:G_region1.qss 0.2011453"," protocol_example::mash::chr22:15528699:A:G_region1.qss 4.5483141","","$strong.s: matrix/array [2 x 2]"," Mic_De_Jager_eQTL"," protocol_example::mash::chr22:15528675:A:G_region1.qss 1"," protocol_example::mash::chr22:15528699:A:G_region1.qss 1"," Ast_De_Jager_eQTL"," protocol_example::mash::chr22:15528675:A:G_region1.qss 1"," protocol_example::mash::chr22:15528699:A:G_region1.qss 1","","$random.b: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," protocol_example::mash::chr22:15528319:A:G_region1.qss 0.69777934"," protocol_example::mash::chr22:15529124:A:G_region1.qss 1.32852955"," protocol_example::mash::chr22:15528227:A:G_region1.qss -0.05627064"," Ast_De_Jager_eQTL"," protocol_example::mash::chr22:15528319:A:G_region1.qss -0.1991450"," protocol_example::mash::chr22:15529124:A:G_region1.qss -0.2385934"," protocol_example::mash::chr22:15528227:A:G_region1.qss 0.9808774","","$random.s: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," protocol_example::mash::chr22:15528319:A:G_region1.qss 1"," protocol_example::mash::chr22:15529124:A:G_region1.qss 1"," protocol_example::mash::chr22:15528227:A:G_region1.qss 1"," Ast_De_Jager_eQTL"," protocol_example::mash::chr22:15528319:A:G_region1.qss 1"," protocol_example::mash::chr22:15529124:A:G_region1.qss 1"," protocol_example::mash::chr22:15528227:A:G_region1.qss 1","","$null.b: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," protocol_example::mash::chr22:15528612:A:G_region1.qss 1.66040624"," protocol_example::mash::chr22:15528787:A:G_region1.qss -0.01514105"," protocol_example::mash::chr22:15529068:A:G_region1.qss 1.63336444"," Ast_De_Jager_eQTL"," protocol_example::mash::chr22:15528612:A:G_region1.qss -1.0569069"," protocol_example::mash::chr22:15528787:A:G_region1.qss -0.9860239"," protocol_example::mash::chr22:15529068:A:G_region1.qss 0.1641178","","$null.s: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," protocol_example::mash::chr22:15528612:A:G_region1.qss 1"," protocol_example::mash::chr22:15528787:A:G_region1.qss 1"," protocol_example::mash::chr22:15529068:A:G_region1.qss 1"," Ast_De_Jager_eQTL"," protocol_example::mash::chr22:15528612:A:G_region1.qss 1"," protocol_example::mash::chr22:15528787:A:G_region1.qss 1"," protocol_example::mash::chr22:15529068:A:G_region1.qss 1"]},"tests/fixtures/mash/expected/mash_input.fmr.rds":{"kind":"rds","lines":["Object: list [length 10]"," Components: strong.b, strong.s, random.b, random.s, null.b, null.s, random.z, null.z, ...","$strong.b: matrix/array [1 x 2]"," Mic_De_Jager_eQTL Ast_De_Jager_eQTL"," [1,] 2.70564 0.5429115","","$strong.s: matrix/array [1 x 2]"," Mic_De_Jager_eQTL Ast_De_Jager_eQTL"," [1,] 1 1","","$random.b: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," chr22:15528319:A:G_protocol_example.QtlFineMappingResult 0.69777934"," chr22:15529124:A:G_protocol_example.QtlFineMappingResult 1.32852955"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult -0.05627064"," Ast_De_Jager_eQTL"," chr22:15528319:A:G_protocol_example.QtlFineMappingResult -0.1991450"," chr22:15529124:A:G_protocol_example.QtlFineMappingResult -0.2385934"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult 0.9808774","","$random.s: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," chr22:15528319:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15529124:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult 1"," Ast_De_Jager_eQTL"," chr22:15528319:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15529124:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult 1","","$null.b: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," chr22:15528612:A:G_protocol_example.QtlFineMappingResult 1.66040624"," chr22:15528787:A:G_protocol_example.QtlFineMappingResult -0.01514105"," chr22:15529068:A:G_protocol_example.QtlFineMappingResult 1.63336444"," Ast_De_Jager_eQTL"," chr22:15528612:A:G_protocol_example.QtlFineMappingResult -1.0569069"," chr22:15528787:A:G_protocol_example.QtlFineMappingResult -0.9860239"," chr22:15529068:A:G_protocol_example.QtlFineMappingResult 0.1641178","","$null.s: matrix/array [15 x 2]"," Mic_De_Jager_eQTL"," chr22:15528612:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528787:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15529068:A:G_protocol_example.QtlFineMappingResult 1"," Ast_De_Jager_eQTL"," chr22:15528612:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528787:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15529068:A:G_protocol_example.QtlFineMappingResult 1"]},"tests/fixtures/mash/expected/mash_input.indep.rds":{"kind":"rds","lines":["Object: list [length 10]"," Components: strong.b, strong.s, random.b, random.s, null.b, null.s, random.z, null.z, ...","$strong.b: matrix/array [1 x 2]"," Mic_De_Jager_eQTL Ast_De_Jager_eQTL"," [1,] 2.70564 0.5429115","","$strong.s: matrix/array [1 x 2]"," Mic_De_Jager_eQTL Ast_De_Jager_eQTL"," [1,] 1 1","","$random.b: matrix/array [10 x 2]"," Mic_De_Jager_eQTL"," chr22:15528791:A:G_protocol_example.QtlFineMappingResult 0.8741938"," chr22:15528516:A:G_protocol_example.QtlFineMappingResult -2.8592052"," chr22:15528699:A:G_protocol_example.QtlFineMappingResult 0.3039547"," Ast_De_Jager_eQTL"," chr22:15528791:A:G_protocol_example.QtlFineMappingResult -0.0510958"," chr22:15528516:A:G_protocol_example.QtlFineMappingResult -1.2528124"," chr22:15528699:A:G_protocol_example.QtlFineMappingResult 4.5483141","","$random.s: matrix/array [10 x 2]"," Mic_De_Jager_eQTL"," chr22:15528791:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528516:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528699:A:G_protocol_example.QtlFineMappingResult 1"," Ast_De_Jager_eQTL"," chr22:15528791:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528516:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528699:A:G_protocol_example.QtlFineMappingResult 1","","$null.b: matrix/array [9 x 2]"," Mic_De_Jager_eQTL"," chr22:15528467:A:G_protocol_example.QtlFineMappingResult 0.57965162"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult -0.05627064"," chr22:15528746:A:G_protocol_example.QtlFineMappingResult 1.10137261"," Ast_De_Jager_eQTL"," chr22:15528467:A:G_protocol_example.QtlFineMappingResult 1.3747398"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult 0.9808774"," chr22:15528746:A:G_protocol_example.QtlFineMappingResult 0.6216373","","$null.s: matrix/array [9 x 2]"," Mic_De_Jager_eQTL"," chr22:15528467:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528746:A:G_protocol_example.QtlFineMappingResult 1"," Ast_De_Jager_eQTL"," chr22:15528467:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528227:A:G_protocol_example.QtlFineMappingResult 1"," chr22:15528746:A:G_protocol_example.QtlFineMappingResult 1"]},"tests/fixtures/mash/expected/mixture_prior.EE.prior.rds":{"kind":"rds","lines":["Object: list [length 3]"," Components: U, w, loglik","$U: list [length 32]"," Components: identity, ALL, Ast, End, Exc, Inh, Mic, OPC, ...","$w: numeric [length 33]"," Values: c(null = 0.350889466152308, identity = 0, ALL = 0, Ast = 0, End = 0.0626903097191792, Exc = 0) ...","$loglik: NULL [length 0]"]},"tests/fixtures/mash/expected/vhat.identity.EE.rds":{"kind":"rds","lines":["Object: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 1 0 0 0 0 0"," [2,] 0 1 0 0 0 0"," [3,] 0 0 1 0 0 0"]},"tests/fixtures/mash/expected/vhat.simple.EE.rds":{"kind":"rds","lines":["Object: matrix/array [8 x 8]"," ALL Ast End Exc Inh Mic"," ALL 1.00000000 0.01420407 -0.06297940 0.65424529 0.01352651 0.2149795"," Ast 0.01420407 1.00000000 0.05708375 0.01527867 0.19794257 -0.1509936"," End -0.06297940 0.05708375 1.00000000 -0.21535872 -0.02215867 -0.3384365"]},"tests/fixtures/mash/expected/vhat.corshrink.EE.rds":{"kind":"rds","lines":["Object: matrix/array [8 x 8]"," ALL Ast End Exc Inh"," ALL 1.0000000000 0.000987488 0.0005125989 6.504117e-01 0.0009814652"," Ast 0.0009874880 1.000000000 0.0014810321 9.971329e-04 0.0078452162"," End 0.0005125989 0.001481032 1.0000000000 9.332334e-05 0.0007185897"," Mic"," ALL 0.0100225824"," Ast 0.0002419493"," End -0.0004634544"]},"tests/fixtures/mash/expected/vhat.simple_specific.EE.rds":{"kind":"rds","lines":["Object: matrix/array [8 x 8]"," ALL Ast End Exc Inh Mic"," ALL 1.000000000 0.009577799 -0.04626552 0.4573655 0.009267642 0.1618731"," Ast 0.009577799 1.000000000 0.04184216 0.0106574 0.135321006 -0.1134433"," End -0.046265520 0.041842160 1.00000000 -0.1636567 -0.016503484 -0.2770151"]},"tests/fixtures/mash/expected/prior.cov_ed.EE.rds":{"kind":"rds","lines":["Object: list [length 3]"," Components: U, w, loglik","$U: list [length 34]"," Components: identity, ALL, Ast, End, Exc, Inh, Mic, OPC, ...","$w: numeric [length 35]"," Values: c(null = 0.350888658143542, identity = 0, ALL = 0, Ast = 0, End = 0.0581579432131964, Exc = 0) ...","$loglik: NULL [length 0]"]},"tests/fixtures/mash/expected/cov.canonical.EE.rds":{"kind":"rds","lines":["Object: list [length 13]"," Components: identity, ALL, Ast, End, Exc, Inh, Mic, OPC, ...","$identity: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 1 0 0 0 0 0"," [2,] 0 1 0 0 0 0"," [3,] 0 0 1 0 0 0","","$ALL: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 1 0 0 0 0 0"," [2,] 0 0 0 0 0 0"," [3,] 0 0 0 0 0 0","","$Ast: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 0 0 0 0 0 0"," [2,] 0 1 0 0 0 0"," [3,] 0 0 0 0 0 0","","$End: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 0 0 0 0 0 0"," [2,] 0 0 0 0 0 0"," [3,] 0 0 1 0 0 0","","$Exc: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 0 0 0 0 0 0"," [2,] 0 0 0 0 0 0"," [3,] 0 0 0 0 0 0","","$Inh: matrix/array [8 x 8]"," [,1] [,2] [,3] [,4] [,5] [,6]"," [1,] 0 0 0 0 0 0"," [2,] 0 0 0 0 0 0"," [3,] 0 0 0 0 0 0"]},"tests/fixtures/mash/expected/cov.pca.EE.rds":{"kind":"rds","lines":["Object: list [length 4]"," Components: PCA_1, PCA_2, PCA_3, tPCA","$PCA_1: matrix/array [8 x 8]"," ALL Ast End Exc Inh Mic"," ALL 0.006180290 0.008174521 0.008739213 -0.007784481 0.003495496 0.02409971"," Ast 0.008174521 0.010812242 0.011559147 -0.010296345 0.004623408 0.03187610"," End 0.008739213 0.011559147 0.012357649 -0.011007613 0.004942791 0.03407809","","$PCA_2: matrix/array [8 x 8]"," ALL Ast End Exc Inh Mic"," ALL 0.02563814 0.03520979 0.1427297 0.03855221 0.004478845 0.01598269"," Ast 0.03520979 0.04835487 0.1960158 0.05294513 0.006150959 0.02194960"," End 0.14272971 0.19601585 0.7945883 0.21462338 0.024934105 0.08897698","","$PCA_3: matrix/array [8 x 8]"," ALL Ast End Exc Inh Mic"," ALL 0.17897232 -0.020181322 -0.15323506 0.17052991 0.071118778 0.12859069"," Ast -0.02018132 0.002275691 0.01727913 -0.01922934 -0.008019513 -0.01450018"," End -0.15323506 0.017279130 0.13119896 -0.14600671 -0.060891483 -0.11009860","","$tPCA: matrix/array [8 x 8]"," ALL Ast End Exc Inh Mic"," ALL 0.021681724 0.005798827 0.01206837 0.020227268 0.0078675632 0.019209544"," Ast 0.005798827 0.010575083 0.03695715 0.005074851 0.0012659803 0.008948697"," End 0.012068372 0.036957148 0.14821781 0.020771536 -0.0002572156 0.012099821"]},"tests/fixtures/mash/expected/cov.flash.EE.rds":{"kind":"rds","lines":["Object: list [length 0]"]},"tests/fixtures/mash/expected/cov.flash_nonneg.EE.rds":{"kind":"rds","lines":["Object: list [length 0]"]},"tests/fixtures/phenotype_formatting/regions.txt":{"kind":"table","rows":[["chr22","10939387","30861524","region1"],["chr22","30861524","50783661","region2"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/tad_list.txt":{"kind":"table","rows":[["#chr","start","end","index"],["chr22","10700000","12700000","TAD_1"],["chr22","13000000","15000000","TAD_2"],["chr22","15200000","17200000","TAD_3"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/keep_samples.txt":{"kind":"table","rows":[["SAMPLE_002"],["SAMPLE_003"],["SAMPLE_004"],["SAMPLE_005"]],"shownColumns":1,"totalColumns":1,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/expected/protocol_example.chr22.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","10939387","10961337","ENSG00000283047","37.0768403309204","0.0","5.5832744229102","0.0"],["chr22","15528191","15529138","ENSG00000130538","0.0","1.08358035439567","8.91397741376836","4.08850454279024"],["chr22","15611758","15613095","ENSG00000231565","5.97808406328782","0.0","2.63711285656005","10.4666167292313"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_chrom_files.txt":{"kind":"table","rows":[["#id","#dir"],["22","protocol_example.genotype.chr22.bed.gz"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_chrom_files.region_list.txt":{"kind":"table","rows":[["#chr","start","end","ID","path"],["chr22","10939387","10961337","ENSG00000283047","protocol_example.genotype.chr22.bed.gz"],["chr22","15528191","15529138","ENSG00000130538","protocol_example.genotype.chr22.bed.gz"],["chr22","15611758","15613095","ENSG00000231565","protocol_example.genotype.chr22.bed.gz"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region/protocol_example.region1.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","10939387","10961337","ENSG00000283047","37.0768403309204","0.0","5.5832744229102","0.0"],["chr22","15528191","15529138","ENSG00000130538","0.0","1.08358035439567","8.91397741376836","4.08850454279024"],["chr22","15611758","15613095","ENSG00000231565","5.97808406328782","0.0","2.63711285656005","10.4666167292313"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_formatting/expected/regions_phenotype_by_region/protocol_example.region2.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","30693781","30907823","ENSG00000184792","23.2978326159215","20.9704714755826","8.35869341969442","16.066159402042"],["chr22","30902218","30902780","ENSG00000237977","0.0","0.0","8.86506705966064","7.69079135082964"],["chr22","30971004","30971148","ENSG00000276664","0.0","0.0","0.0","2.83932127114085"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_formatting/expected/protocol_example.phenotype_by_region_files.txt":{"kind":"table","rows":[["#id","dir"],["region1","protocol_example.region1.bed.gz"],["region2","protocol_example.region2.bed.gz"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/expected/protocol_example.tpm.sample_matched.gct.gz":{"kind":"table","rows":[["#1.2"],["300","6"],["gene_ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000284070","4.46908614068004","3.6324384389436","0","0.926449274182614","8.44864560635242","16.3456237133014","4.07740959667351"]],"shownColumns":8,"totalColumns":8,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/expected/protocol_example.rnaseq.bed.bed.gz.tad_list.txt.2_pheno_per_region.region_list":{"kind":"table","rows":[["#chr","start","end","ID","path"],["chr22","15200000","17200000","TAD_3","protocol_example.rnaseq.bed.bed.gz"],["chr22","17500000","19500000","TAD_4","protocol_example.rnaseq.bed.bed.gz"],["chr22","20000000","22000000","TAD_5","protocol_example.rnaseq.bed.bed.gz"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/phenotype_formatting/expected/protocol_example.chr22.gct":{"kind":"table","rows":[["ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000283047","37.0768403309204","0.0","5.5832744229102","0.0","11.7772567385319","0.0","0.0"],["ENSG00000130538","0.0","1.08358035439567","8.91397741376836","4.08850454279024","4.14014751640196","0.0","0.0"],["ENSG00000231565","5.97808406328782","0.0","2.63711285656005","10.4666167292313","17.4660449424069","9.70082378235877","5.58310234009874"]],"shownColumns":8,"totalColumns":61,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/protocol_example.protein.missing.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","NA","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.EBMF.imputed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","-0.0331401044676228","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.knn.imputed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","-0.703447297160565","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.mean.imputed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","0.0391333975132811","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.lod.imputed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","-2.19704153370897","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.soft.imputed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","-0.288590023075699","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/phenotype_imputation/expected/protocol_example.protein.missing.filtered.imputed.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr12","752578","752579","chr12_ENSG00000060237_Q9H4A3","0.238966360190167","-0.611171227886468","1.3490429933426","-0.715826631844247"],["chr12","990508","990509","chr12_ENSG00000082805_Q8IUD2","-0.288696212799218","-1.86313205860919","1.5453240459519","-0.383786219454044"],["chr12","2794969","2794970","chr12_ENSG00000004478_Q02790","-1.17242006085983","-0.938018529427372","1.20370232963285","-1.31721998132157"]],"shownColumns":8,"totalColumns":64,"truncatedColumns":true},"tests/fixtures/pseudobulk_preprocessing/protocol_example.snrnaseq.seurat_MIC.rds":{"kind":"rds","lines":["Object: Seurat [13326 x 498]","@assays: list [length 1]"," Components: RNA","@meta.data: data.frame [498 x 5]"," orig.ident nCount_RNA nFeature_RNA celltype"," AAACCCACAAATGGTA_SAMPLE_001 SeuratProject 3198 1762 MIC"," AAAGAACTCATGAGGG_SAMPLE_001 SeuratProject 664 537 MIC"," AAAGGGCCAAGACCTT_SAMPLE_001 SeuratProject 2532 1551 MIC"," sample"," AAACCCACAAATGGTA_SAMPLE_001 SAMPLE_001"," AAAGAACTCATGAGGG_SAMPLE_001 SAMPLE_001"," AAAGGGCCAAGACCTT_SAMPLE_001 SAMPLE_001","","@active.assay: character [length 1]"," Values: \"RNA\"","@active.ident: factor [length 498]"," Values: structure(c(AAACCCACAAATGGTA_SAMPLE_001 = 1L, AAAGAACTCATGAGGG_SAMPLE_001 = 1L, AAAGGGCCAAGACCTT_SAMPLE_001 = 1L, AAAGGTAAGGGTACAC_SAMPLE_001 = 1L, AAAGTGATCTTGTTAC_SAMPLE_001 = 1L, AAATGGATCCTTCAGC_SAMPLE_001 = 1L ), levels = \"SeuratProject\", class = \"factor\") ...","@graphs: list [length 0]","@neighbors: list [length 0]"]},"tests/fixtures/pseudobulk_preprocessing/counts_MIC.csv.gz":{"kind":"table","rows":[["","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000000001","299","172","139","269","742","166","696"],["ENSG00000000002","533","624","49","2","1911","1822","679"],["ENSG00000000003","266","1254","2","96","69","87","474"]],"shownColumns":8,"totalColumns":51,"truncatedColumns":true},"tests/fixtures/pseudobulk_preprocessing/atac_MIC_residuals.txt":{"kind":"table","rows":[["","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["chr1-1000-1500","10.5316181036712","10.0782299856604","9.69847909370219","10.0321840665649","11.3624460645551","9.45339725517175","12.0088417718896"],["chr2-3000-3500","9.94704712753556","10.5923588918617","8.97464386590436","4.12683911798198","12.9509486373231","12.0693603093802","11.5287773654627"],["chr3-5000-5500","9.78294652491996","10.7874376477326","3.58479392625449","8.67490986347327","7.72750502355238","8.37133122984549","9.73624986316538"]],"shownColumns":8,"totalColumns":51,"truncatedColumns":true},"tests/fixtures/pseudobulk_preprocessing/expected/expected_counts_MIC.remapped.csv.gz":{"kind":"table","rows":[["","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000000001","299","172","139","269","742","166","696"],["ENSG00000000002","533","624","49","2","1911","1822","679"],["ENSG00000000003","266","1254","2","96","69","87","474"]],"shownColumns":8,"totalColumns":51,"truncatedColumns":true},"tests/fixtures/pseudobulk_preprocessing/expected/expected_MIC_residuals_qn.txt":{"kind":"table","rows":[["","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["ENSG00000000001","0.273701889612983","-0.0245772610640276","-0.273701889612983","-0.0737912738082727","0.786845099455005","-0.430727299295457","1.41570209380051"],["ENSG00000000002","-0.541395085129088","-0.0245772610640276","-1.00743560128731","-1.75986102793353","1.5647264713618","0.928899491647271","0.599229868099345"],["ENSG00000000003","0.377391943828554","0.721522283982343","-2.06191650080946","-0.430727299295457","-0.928899491647271","-0.599229868099345","0.273701889612983"]],"shownColumns":8,"totalColumns":51,"truncatedColumns":true},"tests/fixtures/qtl_association_postprocessing/protocol_example.cis_qtl.pairs.tsv.gz":{"kind":"table","rows":[["chrom","pos","molecular_trait_id","variant_id","tss_distance","tes_distance","af","ma_samples"],["22","10685239","ENSG00000283047","chr22:10685239_C_T","-254149","-276098","0.058333334","7"],["22","10761227","ENSG00000283047","chr22:10761227_G_A","-178161","-200110","0.15","18"],["22","11285239","ENSG00000283047","chr22:11285239_C_T","345851","323902","0.083333336","10"]],"shownColumns":8,"totalColumns":15,"truncatedColumns":true},"tests/fixtures/qtl_association_postprocessing/protocol_example.cis_qtl.regional.tsv.gz":{"kind":"table","rows":[["chrom","pos","n_variants","beta_shape1","beta_shape2","true_df","p_true_df","variant_id"],["22","11797697","6","0.9714302","5.6756625","29.047987","0.03418384894248458","chr22:11797697_C_T"],["22","15838003","51","1.0111347","30.198004","28.527073","0.01017646989997189","chr22:15838003_CTTTCTTTTTCTTT_ATTTCTTTTTCTTT"],["22","15838010","49","0.9969245","25.608551","27.582878","0.04197258326039418","chr22:15838010_TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC_TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC"]],"shownColumns":8,"totalColumns":21,"truncatedColumns":true},"tests/fixtures/qtl_association_postprocessing/protocol_example.maf_0.01_window_1000000_cis_n_variants_stats.tsv.gz":{"kind":"table","rows":[["chrom","molecular_trait_object_id","n_variants","n_variants_filtered"],["chr22","ENSG00000099968","114","114"],["chr22","ENSG00000130538","43","43"],["chr22","ENSG00000215270","51","51"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/qtl_association_postprocessing/expected/qap.cis_regional.fdr.tsv.gz":{"kind":"table","rows":[["chrom","pos","n_variants","beta_shape1","beta_shape2","true_df","p_true_df","variant_id"],["22","11797697","6","0.9714302","5.6756625","29.047987","0.03418384894248458","chr22:11797697_C_T"],["22","15838003","51","1.0111347","30.198004","28.527073","0.01017646989997189","chr22:15838003_CTTTCTTTTTCTTT_ATTTCTTTTTCTTT"],["22","15838010","49","0.9969245","25.608551","27.582878","0.04197258326039418","chr22:15838010_TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC_TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC"]],"shownColumns":8,"totalColumns":31,"truncatedColumns":true},"tests/fixtures/qtl_association_postprocessing/expected/qap.summary.tsv":{"kind":"table","rows":[["method","significant_events","significant_qtl"],["permutation","0","0"],["bonferroni_original","0","0"],["bonferroni_filtered","0","0"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/reference_data_preparation/hgnc_chr22.tsv.gz":{"kind":"table","rows":[["Approved symbol","Previous symbols","Alias symbols","Chromosome","Ensembl gene ID","Ensembl ID(supplied by Ensembl)"],["A4GALT","P1","A14GALT, Gb3S, P(k)","22q13.2","ENSG00000128274","ENSG00000128274"],["ABCD1P4","","","22q11.1","ENSG00000225293","ENSG00000225293"],["ABHD17AP4","FAM108A5, FAM108A5P","","22q11.21","ENSG00000229107","ENSG00000229107"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/reference_data_preparation/mini.gff3":{"kind":"table","rows":[["##gff-version 3"],["22","havana","gene","1000","5000",".","+","."],["22","havana","mRNA","1000","5000",".","+","."],["22","havana","exon","1000","2000",".","+","."]],"shownColumns":8,"totalColumns":9,"truncatedColumns":true},"tests/fixtures/reference_data_preparation/ERCC92.gtf":{"kind":"table","rows":[["ERCC-00002","ERCC","exon","1","1061","0.000000","+","."],["ERCC-00003","ERCC","exon","1","1023","0.000000","+","."],["ERCC-00004","ERCC","exon","1","523","0.000000","+","."],["ERCC-00009","ERCC","exon","1","984","0.000000","+","."]],"shownColumns":8,"totalColumns":9,"truncatedColumns":true},"tests/fixtures/reference_data_preparation/expected/hg_reference_1.filtered.fasta":{"kind":"table","rows":[[">chr22","normal"],["ACGTACGTACGT"],[">chr1_KI270706v1_random","rnd"],["TTTTTTTT"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/reference_data_preparation/expected/hg_gtf_1.reformatted.gtf":{"kind":"table","rows":[["22","havana","gene","15749156","15750825",".","-","."],["22","havana","transcript","15749156","15750825",".","-","."],["22","havana","exon","15750372","15750825",".","-","."],["22","havana","exon","15749156","15749798",".","-","."]],"shownColumns":8,"totalColumns":9,"truncatedColumns":true},"tests/fixtures/reference_data_preparation/expected/faidx.test_contigs.fa.fai":{"kind":"table","rows":[["chr22","12","14","12","13"],["chr1_KI270706v1_random","8","55","8","9"],["chr19_KI270938v1_alt","8","96","8","9"],["HLA-A*01:01:01:01","8","128","8","9"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/reference_data_preparation/expected/mini.gtf":{"kind":"table","rows":[["##gff-version 2"],["##source-version rtracklayer 1.70.1"],["##date 2026-08-13"],["22","havana","transcript","1000","5000",".","+","."]],"shownColumns":8,"totalColumns":9,"truncatedColumns":true},"tests/fixtures/reference_data_preparation/expected/hg38.chr22_SE_strict.ioe":{"kind":"table","rows":[["seqname","gene_id","event_id","alternative_transcripts","total_transcripts"],["chr22","ENSG00000075234","ENSG00000075234;SE:chr22:46268591-46269142:46269289-46272335:+","ENST00000417709","ENST00000381031,ENST00000417709,ENST00000421359"],["chr22","ENSG00000075234","ENSG00000075234;SE:chr22:46281718-46281971:46282151-46283973:+","ENST00000422713","ENST00000381031,ENST00000422713"],["chr22","ENSG00000075234","ENSG00000075234;SE:chr22:46289899-46292203:46292328-46292791:+","ENST00000451998","ENST00000381031,ENST00000451998"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/reference_data_preparation/expected/chr22.SUPPA_annotation.rds":{"kind":"rds","lines":["Object: list [length 7]"," Components: Alternative 3' splice site, Alternative 5' splice site, Alternative first exon, Alternative last exon, Mutually exclusive exon, Retained intron, Skipped exon","$Alternative 3' splice site: data.frame [66 x 7]"," Chromosome Strand Gene Constitutive exon 1 end"," 2 22 - ENSG00000099899 20112911"," 3 22 - ENSG00000099899 20113686"," 1 22 - ENSG00000099899 20114761"," Alternative exon 1 start Alternative exon 2 start"," 2 20112794 20112816"," 3 20113507 20113561"," 1 20114681 20114685","","$Alternative 5' splice site: data.frame [22 x 7]"," Chromosome Strand Gene Alternative exon 1 end"," 78 22 + ENSG00000099968 17638886"," 79 22 + ENSG00000284294 18939757"," 67 22 - ENSG00000099899 20112911"," Alternative exon 2 end Constitutive exon 2 start"," 78 17638700 17655662"," 79 18939749 18946791"," 67 20112956 20112794","","$Alternative first exon: data.frame [109 x 9]"," Chromosome Strand Gene Alternative exon 1 start"," 113 22 + ENSG00000100181 16601887"," 114 22 + ENSG00000100181 16601887"," 115 22 + ENSG00000099968 17628855"," Alternative exon 1 end Alternative exon 2 start"," 113 16602215 16637020"," 114 16602215 16637040"," 115 17628906 17628916","","$Alternative last exon: data.frame [64 x 9]"," Chromosome Strand Gene Constitutive exon 1 end"," 214 22 + ENSG00000100181 16638740"," 215 22 + ENSG00000100181 16638740"," 213 22 + ENSG00000100181 16638740"," Alternative exon 1 start Alternative exon 1 end"," 214 16639298 16640737"," 215 16639298 16640737"," 213 16648527 16653809","","$Mutually exclusive exon: data.frame [18 x 10]"," Chromosome Strand Gene Constitutive exon 1 end"," 269 22 + ENSG00000099968 17655832"," 267 22 + ENSG00000099968 17683321"," 270 22 + ENSG00000099968 17683321"," Alternative exon 1 start Alternative exon 1 end"," 269 17683214 17683321"," 267 17688986 17689142"," 270 17688986 17689142","","$Retained intron: data.frame [13 x 8]"," Chromosome Strand Gene Constitutive exon 1 start"," 287 22 + ENSG00000099942 20949711"," 288 22 + ENSG00000133460 23882759"," 289 22 + ENSG00000133460 23882759"," Constitutive exon 1 end Constitutive exon 2 start"," 287 20949927 20953206"," 288 23882869 23883874"," 289 23882869 23883949"]},"tests/fixtures/rss_analysis/protocol_example.rss_mwe.gwas_meta.tsv":{"kind":"table","rows":[["study_id","path","column_mapping","n_case","n_control"],["AD_Bellenguez_2022","protocol_example.gwas_sumstats.chr22.tsv.gz","protocol_example.gwas_column_mapping.yml","111326","677663"]],"shownColumns":5,"totalColumns":5,"truncatedColumns":false},"tests/fixtures/rss_analysis/protocol_example.gwas_sumstats.chr22.tsv.gz":{"kind":"table","rows":[["#chrom","pos","variant_id","A1","A2","Var","raiss_ld_score","raiss_R2"],["22","49000033","22:49000033:G:A","A","G","-1","Inf","NA"],["22","49000054","22:49000054:G:T","T","G","-1","Inf","NA"],["22","49000336","22:49000336:G:A","A","G","-1","Inf","NA"]],"shownColumns":8,"totalColumns":19,"truncatedColumns":true},"tests/fixtures/rss_analysis/protocol_example.gwas_column_mapping.yml":{"kind":"table","rows":[["chrom:","chrom"],["pos:","pos"],["A1:","A1"],["A2:","A2"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/rss_ld_sketch/protocol_example.ld_blocks.bed":{"kind":"table","rows":[["#chr","start","end"],["chr22","16000000","20000000"],["chr22","30000000","34000000"],["chr22","44000000","48000000"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/rss_ld_sketch/protocol_example.genotype.chr22.vcf.gz":{"kind":"table","rows":[["##fileformat=VCFv4.2"],["##FILTER="],["##fileDate=20231023"],["##source=PLINKv1.90"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/sldsc_enrichment/target.tsv":{"kind":"table","rows":[["chr","pos"],["1","888659"],["1","2974852"],["1","3168280"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/sldsc_enrichment/reference.2.bim":{"kind":"table","rows":[["2","rs10865542","1.2160932","1081594","G","T"],["2","rs13015040","2.5067138","1861586","G","A"],["2","rs719876","4.0279336","2654789","G","A"],["2","rs934558","4.7502589","2871548","T","G"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/sldsc_enrichment/expected/sldsc_postprocess.rds":{"kind":"rds","lines":["Object: list [length 3]"," Components: per_trait, meta, params","$per_trait: list [length 3]"," Components: sumstats.parquet, sumstats2.parquet, sumstats3.parquet","$meta: list [length 3]"," Components: tauStar, enrichment, enrichstat","$params: list [length 7]"," Components: maf_cutoff, M_ref, target_categories, n_baseline, baseline_categories, trait_names, target_categories_orig"]},"tests/fixtures/sldsc_enrichment/expected/sldsc_meta_subset.rds":{"kind":"rds","lines":["Object: list [length 4]"," Components: tau_star_single, tau_star_joint, enrichment, enrichstat","$tau_star_single: list [length 1]"," Components: ANNOT_0","$tau_star_joint: list [length 1]"," Components: ANNOT_0","$enrichment: list [length 1]"," Components: ANNOT_0","$enrichstat: list [length 1]"," Components: ANNOT_0"]},"tests/fixtures/sldsc_enrichment/expected/sldsc_meta_subset.notebook.rds":{"kind":"rds","lines":["Object: list [length 4]"," Components: tau_star_single, tau_star_joint, enrichment, enrichstat","$tau_star_single: list [length 1]"," Components: ANNOT_0","$tau_star_joint: list [length 1]"," Components: ANNOT_0","$enrichment: list [length 1]"," Components: ANNOT_0","$enrichstat: list [length 1]"," Components: ANNOT_0"]},"tests/fixtures/snrnaseq_preprocessing/protocol_example.snrnaseq.seurat_ref_SE.rds":{"kind":"rds","lines":["Object: SummarizedExperiment [length 13326]","@colData: DFrame [1050 x 1]","@assays: SimpleAssays [13326 x 1050]","@NAMES: character [length 13326]"," Values: c(\"NOC2L\", \"KLHL17\", \"HES4\", \"ISG15\", \"AGRN\", \"C1orf159\") ...","@elementMetadata: DFrame [13326 x 0]","@metadata: list [length 0]"]},"tests/fixtures/snrnaseq_preprocessing/protocol_example.snrnaseq.id_mapping.csv":{"kind":"table","rows":[["libraryBatch","cellBarcode","individualID"],["200225-B10-A","AAACGCTCAGACGATG-1","R6249698"],["200225-B10-A","AAAGAACCAGTTTCGA-1","R7840275"],["200225-B10-A","AAATGGAGTATCGTGT-1","R7698313"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/splicing_calling/leafcutter/SAMPLE_001.junc.gz":{"kind":"table","rows":[["chr22","11869845","11873926","JUNC00000001","1","+","11869845","11873926"],["chr22","11873885","11876132","JUNC00000002","1","+","11873885","11876132"],["chr22","11876103","11876296","JUNC00000003","2","+","11876103","11876296"],["chr22","11876223","11882340","JUNC00000004","3","+","11876223","11882340"]],"shownColumns":8,"totalColumns":12,"truncatedColumns":true},"tests/fixtures/splicing_calling/leafcutter/SAMPLE_002.junc.gz":{"kind":"table","rows":[["chr22","11478670","11478844","JUNC00000001","1","-","11478670","11478844"],["chr22","11478790","11479030","JUNC00000002","2","-","11478790","11479030"],["chr22","11903069","11903829","JUNC00000003","1","+","11903069","11903829"],["chr22","12314778","12319531","JUNC00000004","23","-","12314778","12319531"]],"shownColumns":8,"totalColumns":12,"truncatedColumns":true},"tests/fixtures/splicing_calling/psichomics/expected_junctions.txt":{"kind":"table","rows":[["Junction ID","SAMPLE_001.","SAMPLE_002."],["chr22:11478699:11478784:-","0","1"],["chr22:11478905:11478991:-","0","1"],["chr22:11869898:11873841:+","1","0"]],"shownColumns":3,"totalColumns":3,"truncatedColumns":false},"tests/fixtures/splicing_normalization/raw_data.txt.gz":{"kind":"table","rows":[["#Chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","16671178","16671518","chr22:16671178:16671518:clu_27_-","0.6302521008403361","0.3793103448275862","1.0327868852459017","1.8372093023255813"],["chr22","16671588","16673600","chr22:16671588:16673600:clu_27_-","0.13253012048192772","0.504","0.1794871794871795","0.0410958904109589"],["chr22","16673752","16675123","chr22:16673752:16675123:clu_27_-","0.26153846153846155","0.4430379746835443","0.696969696969697","0.7721518987341772"]],"shownColumns":8,"totalColumns":24,"truncatedColumns":true},"tests/fixtures/splicing_normalization/psi_raw_data.tsv.gz":{"kind":"table","rows":[["ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["SE_22_+_42438332_42438832_42439332_42439832_ENSG00000000000","NA","0.3414","0.1858","NA","0.6358","0.1152","NA"],["SE_22_-_42440332_42440832_42441332_42441832_ENSG00000000001","0.7942","0.1614","0.2509","0.6147","0.9029","0.5694","0.4070"],["SE_22_+_42442332_42442832_42443332_42443832_ENSG00000000002","0.1065","0.1036","0.2354","0.6624","0.4348","0.3327","0.5770"]],"shownColumns":8,"totalColumns":21,"truncatedColumns":true},"tests/fixtures/splicing_normalization/expected.phen_chr22.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","42438332","42440491","chr22:42438332:42440491:clu_1_+","2.6","0.05785123966942149","1.3404255319148937","1.392156862745098"],["chr22","42440604","42445702","chr22:42440604:42445702:clu_1_+","0.36","0.17880794701986755","1.2461538461538462","0.0064516129032258064"],["chr22","42445816","42446163","chr22:42445816:42446163:clu_1_+","0.30097087378640774","0.30275229357798167","0.6062992125984252","0.2740740740740741"]],"shownColumns":8,"totalColumns":24,"truncatedColumns":true},"tests/fixtures/splicing_normalization/expected/expected.prepare_phenotype.ave":{"kind":"table","rows":[["chr22:42438332:42440491:clu_1_+","0.006289308176100629","2.6","0.7474529958081921"],["chr22:42440604:42445702:clu_1_+","0.0064516129032258064","1.2461538461538462","0.5161248157417131"],["chr22:42445816:42446163:clu_1_+","0.11578947368421053","2.085714285714286","0.48602444984606896"],["chr22:38991618:38992398:clu_2_-","0.006369426751592357","14.6","1.780681536897999"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/splicing_normalization/expected/expected.prepare_phenotype.phenotype_file_list.txt":{"kind":"table","rows":[["#chr","#dir"],["chr22","leafcutter_perind.counts.gz.qqnorm_chr22"]],"shownColumns":2,"totalColumns":2,"truncatedColumns":false},"tests/fixtures/twas/protocol_example.twas.gwas_meta.tsv":{"kind":"table","rows":[["study_id","chrom","file_path","sample_size"],["protocol_example_twas_chr22","22","tests/fixtures/twas/protocol_example.twas.gwas_sumstats.chr22.tsv.gz","200000"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/twas/protocol_example.twas.xqtl_meta.tsv":{"kind":"table","rows":[["#chr","start","end","region_id","TSS","original_data","contexts"],["chr22","10000000","19000000","ENSG00000130538","15528191","tests/fixtures/twas/protocol_example.twas.reshaped_toy.chr22_ENSG00000130538.univariate_twas_weights.rds","bulk_rnaseq"]],"shownColumns":7,"totalColumns":7,"truncatedColumns":false},"tests/fixtures/twas/expected/twas.chr22.rds":{"kind":"rds","lines":["Object: GRanges [length 1]","@seqnames: Rle [length 1]","@ranges: IRanges [length 1]","@strand: Rle [length 1]","@seqinfo: Seqinfo [length 1]","@elementMetadata: DFrame [1 x 14]","@elementType: character [length 1]"," Values: \"ANY\""]},"tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bim":{"kind":"table","rows":[["22","chr22:10414272:A:T","0","10414272","A","T"],["22","chr22:10416111:A:T","0","10416111","A","T"],["22","chr22:10416669:A:T","0","10416669","A","T"],["22","chr22:10420511:A:T","0","10420511","A","T"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/qtl_mini/protocol_example.genotype.chr22.fam":{"kind":"table","rows":[["SAMPLE_001","SAMPLE_001","0","0","0","-9"],["SAMPLE_002","SAMPLE_002","0","0","0","-9"],["SAMPLE_003","SAMPLE_003","0","0","0","-9"],["SAMPLE_004","SAMPLE_004","0","0","0","-9"]],"shownColumns":6,"totalColumns":6,"truncatedColumns":false},"tests/fixtures/qtl_mini/example_geneexpr.bed.gz":{"kind":"table","rows":[["#chr","start","end","ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004"],["chr22","10939387","10961338","ENSG00000283047","360","128","203","105"],["chr22","15528191","15529139","ENSG00000130538","125","180","220","195"],["chr22","15611758","15613096","ENSG00000231565","205","173","188","227"]],"shownColumns":8,"totalColumns":53,"truncatedColumns":true},"tests/fixtures/qtl_mini/example_covariates.tsv":{"kind":"table","rows":[["ID","SAMPLE_001","SAMPLE_002","SAMPLE_003","SAMPLE_004","SAMPLE_005","SAMPLE_006","SAMPLE_007"],["sex","1","1","1","0","1","0","1"],["age","67.06","82.92","87.76","64.57","81.62","66.44","75.53"],["PC1","-0.7904","-0.1993","0.3059","2.1952","-0.0345","-0.4571","0.7942"]],"shownColumns":8,"totalColumns":50,"truncatedColumns":true},"tests/fixtures/qtl_mini/association_windows.bed":{"kind":"table","rows":[["#chr","start","end","ID"],["chr22","10439387","11461338","ENSG00000283047"],["chr22","15028191","16029139","ENSG00000130538"],["chr22","15111758","16113096","ENSG00000231565"]],"shownColumns":4,"totalColumns":4,"truncatedColumns":false},"tests/fixtures/tensorqtl/expected/cis_qtl.pairs.tsv.gz":{"kind":"table","rows":[["chrom","pos","molecular_trait_id","variant_id","tss_distance","tes_distance","af","ma_samples"],["22","10414272","ENSG00000283047","chr22:10414272:A:T","-525115","-547066","0.5","37"],["22","10416111","ENSG00000283047","chr22:10416111:A:T","-523276","-545227","0.82653064","16"],["22","10416669","ENSG00000283047","chr22:10416669:A:T","-522718","-544669","0.622449","26"]],"shownColumns":8,"totalColumns":14,"truncatedColumns":true},"tests/fixtures/tensorqtl/expected/cis_qtl.regional.tsv.gz":{"kind":"table","rows":[["chrom","pos","n_variants","beta_shape1","beta_shape2","true_df","p_true_df","variant_id"],["22","10456420","200","0.9921782","197.45865","41.613945","0.0017812020290065426","chr22:10456420:A:T"],["22","15966274","1795","1.0157346","1877.0605","42.30297","0.0009428488229498306","chr22:15966274:A:T"],["22","16138746","1795","1.0108896","1879.0338","42.30057","3.083581953564483e-05","chr22:16138746:A:T"]],"shownColumns":8,"totalColumns":21,"truncatedColumns":true},"tests/fixtures/mash/expected/mash_sumstats.region1.rds":{"kind":"rds","lines":["Object: QtlSumStats [length 5]","@ldSketch: NULL [length 0]","@genome: character [length 1]"," Values: \"GRCh38\"","@qcInfo: list [length 2]"," Components: role, entryAudit","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 2L","@elementType: character [length 1]"," Values: \"ANY\""]},"tests/fixtures/qtl_association_postprocessing/expected/qap.rds":{"kind":"rds","lines":["Object: QtlSumStats [length 19]","@ldSketch: NULL [length 0]","@genome: character [length 1]"," Values: \"hg38\"","@qcInfo: list [length 1]"," Components: associationPostprocess","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 10L","@elementType: character [length 1]"," Values: \"ANY\""]},"tests/fixtures/rss_analysis/expected/gwas_sumstats.rds":{"kind":"rds","lines":["Object: GwasSumStats [length 5]","@ldSketch: GenotypeHandle [length 1]","@genome: character [length 1]"," Values: \"GRCh38\"","@qcInfo: list [length 3]"," Components: timestamp, options, entryAudit","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 1L","@elementType: character [length 1]"," Values: \"ANY\""]},"tests/fixtures/rss_analysis/expected/gwas_finemap.rds":{"kind":"rds","lines":["Object: GwasFineMappingResult [length 5]","@ldSketch: GenotypeHandle [length 1]","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 1L","@elementType: character [length 1]"," Values: \"ANY\"","@elementMetadata: NULL [length 0]","@metadata: list [length 0]"]},"tests/fixtures/twas/expected/gwas_sumstats.chr22.rds":{"kind":"rds","lines":["Object: GwasSumStats [length 3]","@ldSketch: GenotypeHandle [length 1]","@genome: character [length 1]"," Values: \"GRCh38\"","@qcInfo: list [length 3]"," Components: timestamp, options, entryAudit","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 1L","@elementType: character [length 1]"," Values: \"ANY\""]},"tests/fixtures/mnm_regression/expected/univariate_bvsr.rds":{"kind":"rds","lines":["Object: QtlFineMappingResult [length 7]","@ldSketch: NULL [length 0]","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 2L","@elementType: character [length 1]"," Values: \"ANY\"","@elementMetadata: NULL [length 0]","@metadata: list [length 0]"]},"tests/fixtures/mnm_regression/expected/univariate_twas_weights.rds":{"kind":"rds","lines":["Object: TwasWeights [length 7]","@ldSketch: NULL [length 0]","@rownames: NULL [length 0]","@nrows: integer [length 1]"," Values: 20L","@elementType: character [length 1]"," Values: \"ANY\"","@elementMetadata: NULL [length 0]","@metadata: list [length 0]"]}}; function pvEsc(s){return String(s).replace(/[&<>"']/g,c=>({'&':'&','<':'<','>':'>','"':'"',"'":'''}[c]));} function previewHTML(path){const p=PREVIEWS[path];if(!p)return ''; if(p.kind==='summary'||p.kind==='rds')return `

R object preview

${p.lines.map(pvEsc).join('\n')}
`; @@ -649,7 +649,7 @@

Your analysis route

const note=`Showing ${n}${p.truncatedColumns?` of ${p.totalColumns}`:''} columns and ${rows.length} rows.`; return `

${note}

${cells(head,'th')}${body.map(r=>`${cells(r,'td')}`).join('')}
`; } -const FXWF={"mixture_prior":{"mashr_input.rds":["*"],"cov.flash.EE.rds":["flash"],"cov.flash_nonneg.EE.rds":["flash_nonneg"],"cov.pca.EE.rds":["pca"],"cov.canonical.EE.rds":["canonical"],"vhat.identity.EE.rds":["vhat_identity"],"vhat.simple.EE.rds":["vhat_simple"],"vhat.corshrink.EE.rds":["vhat_corshrink_xcondition"],"vhat.simple_specific.EE.rds":["vhat_simple_specific"],"prior.cov_ed.EE.rds":["ed_bovy"],"mixture_prior.EE.prior.rds":["ed_bovy","ud","ud_unconstrained"]},"phenotype_imputation":{"protocol_example.protein.missing.bed.gz":["*"],"protocol_example.protein.missing.filtered.imputed.bed.gz":["bed_filter_na"],"protocol_example.protein.missing.EBMF.imputed.bed.gz":["EBMF"],"protocol_example.protein.missing.knn.imputed.bed.gz":["knn"],"protocol_example.protein.missing.mean.imputed.bed.gz":["mean"],"protocol_example.protein.missing.lod.imputed.bed.gz":["lod"],"protocol_example.protein.missing.soft.imputed.bed.gz":["soft"]},"covariate_hidden_factor":{"covariates.tsv":["*"],"residual.bed.gz":["*"],"Marchenko_PC.gz":["Marchenko_PC"],"Buja_Eyuboglu_PC.gz":["PCA"],"PEER.factors.tsv":["PEER"],"PEER.weights.tsv":["PEER"],"PEER.variance.tsv":["PEER"],"PEER.gz":["PEER"]},"gene_annotation":{"protocol_example.atac.tsv":["annotate_coord"],"protocol_example.rnaseq.bed.gz":["annotate_coord"],"protocol_example.rnaseq.bed.bed.gz":["annotate_coord"],"protocol_example.rnaseq.bed.gene_list.tsv":["annotate_coord"],"protocol_example.rnaseq.bed.region_list.txt":["annotate_coord"],"protocol_example.protein.no_coord.bed.gz":["annotate_coord","annotate_coord_biomart"],"protocol_example.protein.no_coord.gene_list.tsv":["annotate_coord","annotate_coord_biomart"],"protocol_example.protein.no_coord.region_list.txt":["annotate_coord","annotate_coord_biomart"],"protocol_example.atac.bed.gz":["annotate_coord"],"protocol_example.atac.region_list.txt":["annotate_coord"],"protocol_example.leafcutter.intron_count.tsv.leafcutter.clusters_to_genes.txt":["map_leafcutter_cluster_to_gene"],"protocol_example.leafcutter.phenotype.bed.formated.bed.gz":["annotate_leafcutter_isoforms"],"protocol_example.leafcutter.phenotype.bed.phenotype_group.txt":["annotate_leafcutter_isoforms"],"protocol_example.psichomics.phenotype.formated.bed.gz":["annotate_psichomics_isoforms"],"protocol_example.psichomics.phenotype.phenotype_group.txt":["annotate_psichomics_isoforms"]},"mnm_regression":{"univariate_bvsr.rds":["susie_twas"],"univariate_twas_weights.rds":["susie_twas"]}}; +const FXWF={"mixture_prior":{"mashr_input.rds":["*"],"cov.flash.EE.rds":["flash"],"cov.flash_nonneg.EE.rds":["flash_nonneg"],"cov.pca.EE.rds":["pca"],"cov.canonical.EE.rds":["canonical"],"vhat.identity.EE.rds":["vhat_identity"],"vhat.simple.EE.rds":["vhat_simple"],"vhat.corshrink.EE.rds":["vhat_corshrink_xcondition"],"vhat.simple_specific.EE.rds":["vhat_simple_specific"],"prior.cov_ed.EE.rds":["ed_bovy"],"mixture_prior.EE.prior.rds":["ed_bovy","ud","ud_unconstrained"]},"phenotype_imputation":{"protocol_example.protein.missing.bed.gz":["*"],"protocol_example.protein.missing.filtered.imputed.bed.gz":["bed_filter_na"],"protocol_example.protein.missing.EBMF.imputed.bed.gz":["EBMF"],"protocol_example.protein.missing.knn.imputed.bed.gz":["knn"],"protocol_example.protein.missing.mean.imputed.bed.gz":["mean"],"protocol_example.protein.missing.lod.imputed.bed.gz":["lod"],"protocol_example.protein.missing.soft.imputed.bed.gz":["soft"]},"covariate_hidden_factor":{"covariates.tsv":["*"],"residual.bed.gz":["*"],"Marchenko_PC.gz":["Marchenko_PC"],"Buja_Eyuboglu_PC.gz":["PCA"],"PEER.factors.tsv":["PEER"],"PEER.weights.tsv":["PEER"],"PEER.variance.tsv":["PEER"],"PEER.gz":["PEER"]},"gene_annotation":{"protocol_example.atac.tsv":["annotate_coord"],"protocol_example.rnaseq.bed.gz":["annotate_coord"],"protocol_example.rnaseq.bed.bed.gz":["annotate_coord"],"protocol_example.rnaseq.bed.gene_list.tsv":["annotate_coord"],"protocol_example.rnaseq.bed.region_list.txt":["annotate_coord"],"protocol_example.protein.no_coord.bed.gz":["annotate_coord","annotate_coord_biomart"],"protocol_example.protein.no_coord.gene_list.tsv":["annotate_coord","annotate_coord_biomart"],"protocol_example.protein.no_coord.region_list.txt":["annotate_coord","annotate_coord_biomart"],"protocol_example.atac.bed.gz":["annotate_coord"],"protocol_example.atac.region_list.txt":["annotate_coord"],"protocol_example.leafcutter.intron_count.tsv.leafcutter.clusters_to_genes.txt":["map_leafcutter_cluster_to_gene"],"protocol_example.leafcutter.phenotype.bed.formated.bed.gz":["annotate_leafcutter_isoforms"],"protocol_example.leafcutter.phenotype.bed.phenotype_group.txt":["annotate_leafcutter_isoforms"],"protocol_example.psichomics.phenotype.formated.bed.gz":["annotate_psichomics_isoforms"],"protocol_example.psichomics.phenotype.phenotype_group.txt":["annotate_psichomics_isoforms"]},"mnm_regression":{"univariate_bvsr.rds":["susie_twas"],"univariate_twas_weights.rds":["susie_twas"],"protocol_example.genotype.chr22.bed":["*"],"protocol_example.pheno_manifest_context.tsv":["*"],"example_covariates.tsv":["*"],"association_windows.bed":["*"],"protocol_example.ENSG00000283047.multicontext_bvsr.rds":["*"]},"colocboost":{"protocol_example.genotype.chr22.bed":["*"],"protocol_example.pheno_manifest_context.tsv":["*"],"example_covariates.tsv":["*"],"association_windows.bed":["*"],"test_coloc.ENSG00000283047.colocboost.rds":["*"]},"mash_posterior":{"region_strong.rds":["*"],"fine_mapping.rds":["*"],"orig.rds":["*"],"posterior.rds":["*"]},"ld_prune_reference":{"protocol_example.ld_genotype.chr22.bed":["*"],"protocol_example.ld_genotype.list":["*"],"LD_pruned_variants.txt":["*"]},"rss_ld_sketch":{"protocol_example.genotype.chr22.vcf.gz":["*"],"protocol_example.ld_blocks.bed":["*"],"afreq_deterministic.tsv":["*"],"event_id.tsv":["*"]},"snRNAseq_preprocessing":{"protocol_example.snrnaseq.id_mapping.csv":["*"],"protocol_example.snrnaseq.seurat_ref_SE.rds":["*"],"expected_manifest.tsv":["*"]},"RNA_calling":{"protocol_example.rnaseq.fastq.list.txt":["*"],"adapters.fa":["*"],"SAMPLE_001.strand.txt":["*"],"fastq.list.trimmed.txt":["*"],"rnaseqc.rnaseqc.exon_readsCount.gct.gz":["*"],"rnaseqc.rnaseqc.gene_readsCount.gct.gz":["*"],"rnaseqc.rnaseqc.gene_tpm.gct.gz":["*"],"rnaseqc.rnaseqc.metrics.tsv":["*"]},"apa_calling":{"chr22_3UTR.bed":["*"],"expected_3UTR.bed":["*"],"expected_gene_annotation.bed":["*"],"protocol_example.expected_3UTR.bed":["*"],"protocol_example.expected_gene_annotation.bed":["*"],"chr22.hdr.gtf.gz":["*"],"expected_pdui_data.txt":["*"],"expected_transcript_to_geneName.txt":["*"]}}; const TERMNOTES={"reference_data_preparation":[["Reference genome build","The coordinate system and allele reference used to align genotype, annotation, and molecular phenotype data."],["Gene annotation","A catalog that links genomic intervals to genes, transcripts, and other functional features."]],"generalized_TADB":[["Topologically associating domain (TAD)","A genomic region whose DNA sequences interact with one another more often than with sequences outside the region."],["Regulatory domain","The genomic neighborhood in which variants are considered capable of regulating a molecular feature."]],"ld_prune_reference":[["Linkage disequilibrium (LD)","Correlation between alleles at nearby variants caused by their shared inheritance."],["LD pruning","Selection of a comparatively independent subset of variants by removing highly correlated markers."]],"rss_ld_sketch":[["LD matrix","A matrix of correlations among variants in a genomic region."],["Summary-statistics fine-mapping","Inference of causal variants from association statistics and an external LD reference rather than individual-level genotypes."]],"RNA_calling":[["Read alignment","Placement of sequencing reads onto a reference genome or transcriptome."],["Gene-level count","The number of aligned fragments assigned to a gene, used as a measure of RNA abundance."]],"bulk_expression_QC":[["Expression quality control","Detection of samples or genes whose sequencing, mapping, or abundance profiles are inconsistent with the study population."],["Outlier sample","A sample whose molecular profile differs unusually from the rest and may reflect technical failure or biological heterogeneity."]],"bulk_expression_normalization":[["Library-size normalization","Adjustment for differences in sequencing depth and RNA composition across samples."],["Inverse-normal transformation","A rank-based transformation that maps a phenotype to an approximately normal distribution."]],"snRNAseq_preprocessing":[["Single-nucleus RNA sequencing","Measurement of RNA abundance in individual nuclei, often used for frozen tissue."],["Cell type","A biologically defined class of cells or nuclei identified from characteristic expression patterns."]],"pseudobulk_preprocessing":[["Pseudobulk expression","Counts aggregated across cells of the same donor and cell type to create a donor-level molecular phenotype."],["Donor","The individual from whom molecular measurements and genotypes were obtained."]],"splicing_calling":[["Splice junction","A boundary formed when an intron is removed and two exons are joined."],["Intron excision","Removal of an intron from a precursor RNA molecule during splicing."]],"splicing_normalization":[["Intron excision ratio","The relative usage of a splice junction or intron within its local cluster."],["Alternative splicing","Production of different RNA isoforms through differential exon or splice-junction use."]],"methylation_calling":[["DNA methylation","Addition of a methyl group to DNA, commonly measured at CpG sites as an epigenetic regulatory mark."],["Beta value","The estimated fraction of methylated signal at a CpG probe."]],"apa_calling":[["Alternative polyadenylation","Use of different transcript cleavage and polyadenylation sites, which changes the RNA 3-prime end."],["Polyadenylation site","The transcript position at which RNA is cleaved before addition of the poly(A) tail."]],"apa_impute":[["Imputation","Estimation of missing molecular measurements from patterns observed across features and samples."],["Missingness","The pattern and proportion of unavailable measurements in a molecular phenotype matrix."]],"VCF_QC":[["Minor allele frequency (MAF)","The frequency of the less common allele at a variant in the analyzed sample."],["Hardy-Weinberg equilibrium","The expected genotype-frequency relationship under random mating, used as one signal of genotype quality."]],"genotype_formatting":[["Allele harmonization","Alignment of variant identifiers, reference alleles, alternate alleles, and strand orientation across datasets."],["Dosage","The expected number of alternate alleles carried by an individual, often ranging continuously from zero to two after imputation."]],"GWAS_QC":[["Genome-wide association study (GWAS)","A scan for genetic variants associated with a complex trait or disease."],["Genomic inflation","Systematic excess of association signal that can reflect confounding, relatedness, or polygenicity."]],"PCA":[["Population structure","Systematic genetic differences among ancestry groups or subpopulations."],["Genotype principal component","A major axis of genetic variation used to adjust association analyses for population structure."]],"gene_annotation":[["Transcription start site (TSS)","The genomic position where transcription of a gene begins."],["Gene model","The annotated genomic structure of a gene, including its exons, transcripts, and strand."]],"phenotype_imputation":[["Phenotype imputation","Estimation of missing molecular phenotype values using information shared across samples or features."],["Limit of detection","The smallest abundance that an assay can distinguish reliably from background."]],"phenotype_formatting":[["Molecular phenotype","A quantitative molecular trait such as gene expression, splicing, methylation, or protein abundance."],["Genomic interval","A chromosome, start, and end coordinate used to locate a molecular feature."]],"covariate_formatting":[["Covariate","A measured variable included in a model to account for known biological or technical variation."],["Design matrix","A numeric representation of model covariates across samples."]],"covariate_hidden_factor":[["Hidden factor","An unmeasured source of variation, such as cell composition, technical batch, or RNA quality, inferred from the molecular phenotype matrix."],["Confounding","Distortion of a genetic association by a variable related to both the tested genotype and molecular phenotype."]],"TensorQTL":[["xQTL","A genetic variant associated with variation in a molecular phenotype such as expression, splicing, methylation, or protein abundance."],["cis association","An association between a variant and a nearby molecular feature within a defined genomic window."],["False discovery rate (FDR)","The expected proportion of false positives among results declared significant."]],"qr_and_twas":[["Quantile regression","A model that estimates genetic effects at selected points of a phenotype distribution rather than only its mean."],["TWAS weight","An estimated genetic effect used to predict a molecular trait from local variants."]],"qtl_association_postprocessing":[["Lead variant","The variant with the strongest association signal for a molecular feature or region."],["Allelic effect","The direction and magnitude of phenotype change associated with an allele."]],"METAL":[["Meta-analysis","Statistical combination of association evidence across cohorts while allowing each cohort to retain its own participants."],["Heterogeneity","Variation in estimated genetic effects across cohorts or studies."]],"mash_preprocessing":[["Effect-size matrix","A matrix of association estimates arranged across variants or genes and biological conditions."],["Standard error","The estimated uncertainty of an effect-size estimate."]],"mixture_prior":[["Covariance prior","A learned representation of how genetic effects tend to be shared across tissues, cell types, or molecular traits."],["Residual correlation","Correlation among association estimates that remains after accounting for true shared effects."]],"mash_fit":[["Empirical Bayes","A framework that estimates a prior distribution from the observed data and uses it to update noisy effects."],["Shrinkage","Pulling uncertain effect estimates toward patterns supported by the full dataset."],["Local false sign rate","The posterior probability that the reported direction of an effect is wrong."]],"mash_posterior":[["Posterior distribution","The updated probability distribution of an effect after combining the observed data with the fitted prior."],["Posterior contrast","A probabilistic comparison of effects between biological conditions."]],"mnm_regression":[["Fine-mapping","Prioritization of variants that may causally explain an association signal."],["Posterior inclusion probability (PIP)","The posterior probability that a variant contributes to the genetic signal in the fitted model."],["Credible set","A group of variants that jointly contains a causal regulatory variant with a stated posterior probability under the fitted model."]],"rss_analysis":[["Fine-mapping","Prioritization of variants that may causally explain an association signal."],["Posterior inclusion probability (PIP)","The posterior probability that a variant contributes to the genetic signal in the fitted model."],["Credible set","A group of variants that jointly contains a causal regulatory variant with a stated posterior probability under the fitted model."]],"SuSiE_enloc":[["Colocalization","Evidence that molecular-trait and complex-trait associations in a region are explained by the same underlying genetic signal."],["Regional enrichment","Increased probability that a trait-associated region also contains a molecular QTL signal."]],"twas_ctwas":[["Transcriptome-wide association study (TWAS)","A test relating genetically predicted molecular phenotypes to a complex trait."],["Mediated association","A trait association consistent with a genetic effect acting through a measured molecular phenotype."]],"colocboost":[["Colocalization","Evidence that molecular-trait and complex-trait associations in a region are explained by the same underlying genetic signal."],["Multiple causal signals","More than one distinct causal association pattern within the same genomic region."]],"intact":[["Colocalization","Evidence that molecular-trait and complex-trait associations in a region are explained by the same underlying genetic signal."],["Cross-tissue evidence","Association information combined across tissues or molecular contexts."]],"watershed":[["Variant-to-gene prioritization","Ranking variants by evidence that they regulate a particular gene and contribute to disease risk."],["Functional annotation","Biological information about a variant or genomic region used to interpret its potential mechanism."]],"eoo_enrichment":[["Enrichment","An excess of overlap between two sets of genomic signals relative to an appropriate null expectation."],["Observed-to-expected ratio","The observed overlap divided by the overlap expected under a null model."]],"gsea":[["Gene set enrichment analysis (GSEA)","A test for coordinated concentration of association evidence within a predefined group of genes."],["Gene set","A collection of genes sharing a pathway, function, annotation, or experimental signature."]],"gregor":[["Regulatory enrichment","Overrepresentation of associated variants in regulatory annotations compared with matched control variants."],["Matched control variant","A background variant selected to resemble an associated variant in properties such as allele frequency and LD."]],"sldsc_enrichment":[["Stratified LD score regression (S-LDSC)","A method that partitions SNP heritability across genomic annotations using GWAS summary statistics and LD."],["SNP heritability","The proportion of trait variation attributable to the additive effects of measured or tagged variants."]],"ems_training":[["Expression modifier score (EMS)","A learned score estimating the probability that a variant has a regulatory effect on a gene."],["Training label","An observed outcome used to teach a predictive model which genomic patterns distinguish regulatory variants."]],"ems_prediction":[["Expression modifier score (EMS)","A learned score estimating the probability that a variant has a regulatory effect on a gene."],["Calibration","Agreement between predicted probabilities and the observed frequency of the corresponding outcome."]]}; function open(btn){curBtn=btn; const nb=btn.closest('.mw').dataset.nb; cur=nb; initM(nb); diff --git a/code/SoS/xqtl_protocol_workflow_builder.ipynb b/code/SoS/xqtl_protocol_workflow_builder.ipynb index 5e2ac084f..872075adf 100644 --- a/code/SoS/xqtl_protocol_workflow_builder.ipynb +++ b/code/SoS/xqtl_protocol_workflow_builder.ipynb @@ -3,7 +3,754 @@ { "cell_type": "markdown", "metadata": {}, - "source": "# xQTL Analysis Workflow Builder\n\nNot set up yet? Start with [Environment Setup](https://statfungen.github.io/xqtl-protocol/xqtl_protocol_demo.html) to install the software stack and run a first pipeline on the example data shipped in this repository. Each module below links to its own page, where the inputs, expected outputs and full command interface are documented.\n\n\n````{raw} html\n
\n\n\n
\n
\n

xQTL Analysis Workflow Builder

\n

xQTL studies ask how inherited genetic variation changes a molecular phenotype—such as gene expression, splicing, methylation or polyadenylation—and whether that regulatory effect helps explain variation in a complex trait. The map follows that scientific argument from a measured molecular phenotype to a localized regulatory signal and, when appropriate, to evidence connecting the signal with disease biology. Genetic regulation is often tissue- and cell-context-specific, so the relevant path depends on what was measured and where it was measured (GTEx Consortium, 2020).

\n
\n
\n

A practical map of the analysis

\n

From biological samples to interpretable xQTL discoveries

\n

The pipeline turns a broad biological question—does genetic variation alter a molecular process?—into progressively more specific evidence. Not every project needs every stage: the route should match the molecular phenotype, study design and claim being tested.

\n
    \n
  1. 1Define the molecular phenotype

    Turn the assay into biologically interpretable features—expression levels, splice usage, methylation states or polyadenylation usage—in the tissue or cell population relevant to the question. Quality control protects the biological comparison from sample swaps, outliers and poorly measured features.

    2. \n
  2. 2Separate inherited regulation from other variation

    Individuals differ because of ancestry, environment, cell composition and technical effects as well as genotype. Accounting for these sources of variation makes the allelic effect easier to interpret as genetic regulation of the molecular phenotype.

    3. \n
  3. 3Map and localize regulatory effects

    Association testing identifies loci where genotype tracks the molecular phenotype. Multi-context analysis asks whether an effect is shared across tissues or cell types; fine-mapping narrows correlated variants to credible sets that quantify uncertainty rather than declaring a single causal variant (Wang et al., 2020).

    4. \n
  4. 4Relate regulation to complex traits

    Colocalization evaluates whether molecular and trait associations are consistent with a shared causal signal (Giambartolomei et al., 2014), while TWAS tests whether genetically predicted molecular levels are associated with the trait (Gusev et al., 2016). Together with functional enrichment, these analyses prioritize mechanisms but do not by themselves prove mediation or causality.

    5. \n
\n

How to use this page: describe your data and goal, follow the highlighted route, open a module to inspect its real fixture files, and run the displayed sos run command.

\n
\n
\n
\n

Tell us about your data and goal

\n
\n
\n \n \n \n
\n

\n
\n\n

Inputs

Reference Data

Quantification

Molecular Phenotype Quantification

Bulk RNA-seq
Single-nuclei / pseudobulk
Alternative splicing
DNA methylation
Polyadenylation

Pre-processing

Data Pre-processing

Genotype
Phenotype
Covariate

Discovery

QTL Association Testing

Multivariate modelling

Cross-cohort Meta-analysis

Multivariate Mixture (MASH)

Regression

High-dimensional Regression

Individual level
Summary statistics level

Integration

GWAS Integration

Rare-variant xQTL

Interpretation

Enrichment & Validation

xQTL Modifier Score

\n
\n\n\n\n
\n\n\n````\n" + "source": [ + "# xQTL Analysis Workflow Builder\n", + "\n", + "Not set up yet? Start with [Environment Setup](https://statfungen.github.io/xqtl-protocol/xqtl_protocol_demo.html) to install the software stack and run a first pipeline on the example data shipped in this repository. Each module below links to its own page, where the inputs, expected outputs and full command interface are documented.\n", + "\n", + "\n", + "````{raw} html\n", + "
\n", + "\n", + "\n", + "
\n", + "
\n", + "

xQTL Analysis Workflow Builder

\n", + "

xQTL studies ask how inherited genetic variation changes a molecular phenotype—such as gene expression, splicing, methylation or polyadenylation—and whether that regulatory effect helps explain variation in a complex trait. The map follows that scientific argument from a measured molecular phenotype to a localized regulatory signal and, when appropriate, to evidence connecting the signal with disease biology. Genetic regulation is often tissue- and cell-context-specific, so the relevant path depends on what was measured and where it was measured (GTEx Consortium, 2020).

\n", + "
\n", + "
\n", + "

A practical map of the analysis

\n", + "

From biological samples to interpretable xQTL discoveries

\n", + "

The pipeline turns a broad biological question—does genetic variation alter a molecular process?—into progressively more specific evidence. Not every project needs every stage: the route should match the molecular phenotype, study design and claim being tested.

\n", + "
    \n", + "
  1. 1Define the molecular phenotype

    Turn the assay into biologically interpretable features—expression levels, splice usage, methylation states or polyadenylation usage—in the tissue or cell population relevant to the question. Quality control protects the biological comparison from sample swaps, outliers and poorly measured features.

    2. \n", + "
  2. 2Separate inherited regulation from other variation

    Individuals differ because of ancestry, environment, cell composition and technical effects as well as genotype. Accounting for these sources of variation makes the allelic effect easier to interpret as genetic regulation of the molecular phenotype.

    3. \n", + "
  3. 3Map and localize regulatory effects

    Association testing identifies loci where genotype tracks the molecular phenotype. Multi-context analysis asks whether an effect is shared across tissues or cell types; fine-mapping narrows correlated variants to credible sets that quantify uncertainty rather than declaring a single causal variant (Wang et al., 2020).

    4. \n", + "
  4. 4Relate regulation to complex traits

    Colocalization evaluates whether molecular and trait associations are consistent with a shared causal signal (Giambartolomei et al., 2014), while TWAS tests whether genetically predicted molecular levels are associated with the trait (Gusev et al., 2016). Together with functional enrichment, these analyses prioritize mechanisms but do not by themselves prove mediation or causality.

    5. \n", + "
\n", + "

How to use this page: describe your data and goal, follow the highlighted route, open a module to inspect its real fixture files, and run the displayed sos run command.

\n", + "
\n", + "
\n", + "
\n", + "

Tell us about your data and goal

\n", + "
\n", + "
\n", + " \n", + " \n", + " \n", + "
\n", + "

\n", + "
\n", + "\n", + "

Inputs

Reference Data

Quantification

Molecular Phenotype Quantification

Bulk RNA-seq
Single-nuclei / pseudobulk
Alternative splicing
DNA methylation
Polyadenylation

Pre-processing

Data Pre-processing

Genotype
Phenotype
Covariate

Discovery

QTL Association Testing

Multivariate modelling

Cross-cohort Meta-analysis

Multivariate Mixture (MASH)

Regression

High-dimensional Regression

Individual level
Summary statistics level

Integration

GWAS Integration

Rare-variant xQTL

Interpretation

Enrichment & Validation

xQTL Modifier Score

\n", + "
\n", + "\n", + "\n", + "\n", + "
\n", + "\n", + "\n", + "````\n" + ] } ], "metadata": { diff --git a/tests/fixtures/mnm_regression/expected/README.md b/tests/fixtures/mnm_regression/expected/README.md new file mode 100644 index 000000000..f0bd01a13 --- /dev/null +++ b/tests/fixtures/mnm_regression/expected/README.md @@ -0,0 +1,38 @@ +# mnm_regression expected outputs + +| file | produced by | +|---|---| +| `univariate_bvsr.rds` | `susie_twas` — per-context SuSiE fine-mapping (`method = "susie"`) | +| `univariate_twas_weights.rds` | `susie_twas` — TWAS weights from the same run | +| `protocol_example.ENSG00000283047.multicontext_bvsr.rds` | `mnm` — joint multi-context fit (`method = "mvsusie"`, carries a `jointContexts` column) | + +## Regenerating the multicontext result + +`mnm` needs the dataset built first, so run both steps together. Note two things the +module documentation currently gets wrong: the parameter is `--prior`, not +`--mixture-prior`, and `--transpose-covariates True` is required — without it the run +fails with "No shared samples between phenotype and covariate file", which looks like +a data problem but is an orientation one. + +```bash +sos run pipeline/mnm_regression.ipynb qtl_dataset_construct+mnm \ + --name protocol_example --cwd \ + --genoFile tests/fixtures/qtl_mini/protocol_example.genotype.chr22.bed \ + --phenoFile tests/fixtures/qtl_mini/protocol_example.pheno_manifest_context.tsv \ + --covFile tests/fixtures/qtl_mini/example_covariates.tsv \ + --transpose-covariates True \ + --customized-association-windows tests/fixtures/qtl_mini/association_windows.bed \ + --region-name ENSG00000283047 --save-data --no-skip-twas-weights \ + --phenotype-names mv_pheno \ + --prior tests/fixtures/mash/expected/mixture_prior.EE.prior.rds \ + --ld-reference-meta-file tests/fixtures/ld_reference/ld_meta_file.tsv \ + --modular_script_dir code/script -j1 +``` + +The mixture prior is a choice: `tests/fixtures/mash/expected/` also holds +`prior.cov_ed.EE.rds`. This fixture was generated with `mixture_prior.EE.prior.rds`. +If that is not the intended prior for the toy data, regenerate and replace. + +No test currently drives the `mnm` step — `test_mnm_regression` runs +`qtl_dataset_construct+susie_twas` only — so this file is documentation of the +expected shape rather than an asserted comparison. diff --git a/tests/fixtures/mnm_regression/expected/protocol_example.ENSG00000283047.multicontext_bvsr.rds b/tests/fixtures/mnm_regression/expected/protocol_example.ENSG00000283047.multicontext_bvsr.rds new file mode 100644 index 000000000..65db97ce2 Binary files /dev/null and b/tests/fixtures/mnm_regression/expected/protocol_example.ENSG00000283047.multicontext_bvsr.rds differ