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Merged
gaow merged 1 commit into from
Sep 3, 2026
Merged

Default SuSiE L to 10 and greedy-L off #1422

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10 changes: 5 additions & 5 deletions code/SoS/mnm_analysis/mnm_methods/rss_analysis.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,7 @@
"\n",
"- `--methods` (default `susie`), `--coverage` (`0.95`), `--secondary-coverage` (`0.7,0.5`).\n",
"- `--min-abs-corr` (`0.8`), `--median-abs-corr` (off; sets OR-logic purity), `--pip-cutoff` (`0.025`).\n",
"- `--L` (`20`) and `--L-greedy` (`5`): SuSiE fit defaults.\n",
"- `--L` (`10`) and `--L-greedy` (`none`; a positive int enables the greedy-L loop): SuSiE fit defaults.\n",
"- `--method-args`: JSON overriding any of the above per method, e.g. `{\"susie\":{\"L\":10}}`.\n",
"- `--ser-fallback` / `--no-ser-fallback` (default on), `--r-finite`, `--r-mismatch` (`eb_mix`), `--rss-control`: numerical safeguards for the RSS likelihood.\n",
"- `--[no-]keep-original-fit` (default off): retain the pre-fallback multi-effect fit on SER-fallback regions (where it differs from the reported SER fit); off keeps none.\n",
Expand Down Expand Up @@ -306,8 +306,8 @@
" --min-abs-corr 0.8 (as float)\n",
" --median-abs-corr ''\n",
" --pip-cutoff 0.025 (as float)\n",
" --L 20 (as int)\n",
" --L-greedy 5 (as int)\n",
" --L 10 (as int)\n",
" --L-greedy none (as str; positive int enables greedy-L)\n",
" --method-args ''\n",
" --[no-]ser-fallback (default to True)\n",
" GWAS SuSiE-RSS fine-mapping: SER fallback is ON by\n",
Expand Down Expand Up @@ -392,8 +392,8 @@
"parameter: min_abs_corr = 0.8\n",
"parameter: median_abs_corr = '' # empty -> off (OR-logic purity; needs pecotmr step-1)\n",
"parameter: pip_cutoff = 0.025\n",
"parameter: L = 20\n",
"parameter: L_greedy = 5\n",
"parameter: L = 10\n",
"parameter: L_greedy = 'none' # 'none'/'off' = greedy off (default); a positive int enables greedy-L\n",
"parameter: method_args = '' # nested per-method JSON object\n",
"# GWAS SuSiE-RSS fine-mapping: SER fallback is ON by default (reproduces the single-panel notebook):\n",
"# fit finite-sample R + EB LD-mismatch SuSiE-RSS and fall back to the single-effect (SER) result for\n",
Expand Down
28 changes: 23 additions & 5 deletions code/script/pecotmr_integration/fine_mapping.R
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Expand Up @@ -95,11 +95,13 @@ parser <- add_argument(parser, "--pip-cutoff",
help = "PIP signal cutoff (fineMappingPipeline signalCutoff)",
type = "numeric", default = 0.025)
parser <- add_argument(parser, "--L",
help = "SuSiE number of single effects (susie L); pipeline default 20",
type = "integer", default = 20L)
help = "SuSiE number of single effects (susie L); pipeline default 10",
type = "integer", default = 10L)
parser <- add_argument(parser, "--L-greedy",
help = "SuSiE greedy init count (susie L_greedy); pipeline default 5",
type = "integer", default = 5L)
help = paste("SuSiE greedy init count (susie L_greedy): a positive integer to run",
"the greedy-L loop, or 'none'/'off' to disable it; pipeline default",
"none (greedy off)"),
type = "character", default = "none")
parser <- add_argument(parser, "--method-args",
help = "JSON object {token: {kwarg: value, ...}, ...} for fineMappingPipeline()",
type = "character", default = "")
Expand Down Expand Up @@ -245,6 +247,22 @@ secondary_cov <- as.numeric(trimws(strsplit(argv$secondary_coverage, ",", fixed
median_abs_corr <- if (length(argv$median_abs_corr) != 1L || is.na(argv$median_abs_corr))
NULL else argv$median_abs_corr

# L_greedy: 'none'/'off'/'null'/empty (case-insensitive) -> NULL, i.e. greedy-L
# off (susie's own L_greedy default is NULL). Otherwise a positive integer.
# The NULL is kept via the inline list() in cs_args below, which preserves a
# named NULL through c()/do.call to fineMappingPipeline; only an x$Lgreedy <- NULL
# assignment would drop it (re-enabling pecotmr's default 5).
l_greedy_raw <- trimws(argv[["L_greedy"]])
l_greedy_val <- if (tolower(l_greedy_raw) %in% c("none", "off", "null", "")) {
NULL
} else {
v <- suppressWarnings(as.integer(l_greedy_raw))
if (is.na(v) || v < 1L)
stop("--L-greedy must be a positive integer or 'none'/'off' (got: '",
argv[["L_greedy"]], "')")
v
}

# Seed up front for reproducible fits (mirrors the legacy susie_twas set.seed).
# NULL when --seed is unset. In QTL mode the value is ALSO forwarded to the
# pipeline as seed= (below): set.seed() only touches this process's RNG, so it
Expand Down Expand Up @@ -302,7 +320,7 @@ methods_arg <- if (is.null(parsed_method_args)) methods else
# seeds the susie-family tokens and applies explicit --method-args overrides.
cs_args <- list(methods = methods_arg,
L = argv$L,
Lgreedy = argv[["L_greedy"]],
Lgreedy = l_greedy_val,
coverage = argv$coverage,
secondaryCoverage = secondary_cov,
signalCutoff = argv$pip_cutoff,
Expand Down
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