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Prepare ColocBoost 1.0.10: scalability, robustness, and tutorials - #150

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xueweic merged 19 commits into
StatFunGen:mainfrom
xueweic:main
Sep 8, 2026
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Prepare ColocBoost 1.0.10: scalability, robustness, and tutorials#150
xueweic merged 19 commits into
StatFunGen:mainfrom
xueweic:main

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@xueweic xueweic commented Sep 8, 2026

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Summary

This PR prepares ColocBoost 1.0.10 with improvements to computational scalability, robustness, and conceptual documentation. It also addresses the CRAN-reported MKL-sensitive test failure in version 1.0.9.

No package dependencies are added or changed.

Computational scalability

  • Reduced redundant LD calculations, purity evaluations, matrix operations, and memory reallocations.
  • Improved computational efficiency for analyses involving large numbers of phenotypes.

Robustness fixes

  • Improved handling of outcome names and large trait configurations.
  • Addressed edge cases in CoS assembly, output generation, and plotting.
  • Stabilized the CRAN-reported MKL-sensitive tests using stronger simulation signals and aligned test inputs, without skipping the affected tests.

Documentation and tutorials

  • Added a conceptual framework for multi-trait colocalization events and interpretation of CoS, VCP, and NPC.
  • Added advanced examples covering multiple causal variants and weaker disease-GWAS signals.
  • Added six high-level summary figures with empirical results and reorganized vignette-only assets to reduce duplicated installed-package content.

xueweic added 16 commits June 20, 2026 21:25
Prevented ColocBoost inference failures with thousands of phenotypes by replacing oversized configuration names with compact group identifiers.
[v2] Prevented ColocBoost inference failures with thousands of phenotypes by replacing oversized configuration names with compact group identifiers.
Add conceptual and advanced-scenario vignettes and supporting figures for interpreting ColocBoost results.
@xueweic
xueweic requested a review from danielnachun September 8, 2026 15:02
@xueweic
xueweic merged commit 3aa8433 into StatFunGen:main Sep 8, 2026
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