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

Default fineMappingPipeline L to 10 and greedy-L off #592

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17 changes: 9 additions & 8 deletions R/fineMappingPipeline.R
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Original file line number Diff line number Diff line change
Expand Up @@ -255,9 +255,10 @@
#' @param keepVariants Character vector or \code{NULL}. Per-call override of the
#' \code{QtlDataset} variant allow-list; \code{NULL} uses the dataset's stored
#' value.
#' @param L Integer. Maximum number of SuSiE single effects. Default \code{20}.
#' @param Lgreedy Integer. Number of greedily-added effects in the SuSiE-inf
#' refinement. Default \code{5}.
#' @param L Integer. Maximum number of SuSiE single effects. Default \code{10}.
#' @param Lgreedy Integer or \code{NULL}. Number of greedily-added effects in the
#' SuSiE-inf refinement (the greedy-L loop). \code{NULL} (default) disables the
#' greedy loop and fits \code{L} directly.
#' @param twasWeights Optional \code{\link{TwasWeights}} resume cache to reuse
#' previously fitted weights; \code{NULL} fits fresh.
#' @param dataDrivenPriorWeightsCutoff Numeric or \code{NULL}. Cutoff below
Expand Down Expand Up @@ -458,7 +459,7 @@ setGeneric("fineMappingPipeline", function(data, ...) {
# Mirrors the convention of .twasNormalizeMethods so the two pipelines
# expose the same shape on the user side.
# @noRd
.fmNormalizeMethods <- function(methods, L = 20L, Lgreedy = 5L) {
.fmNormalizeMethods <- function(methods, L = 10L, Lgreedy = NULL) {
if (is.null(methods) || length(methods) == 0L) {
msg <- glue(
"fineMappingPipeline: `methods` must be a non-empty character ",
Expand Down Expand Up @@ -2594,8 +2595,8 @@ setMethod(
jointRegions = FALSE,
jointSpecification = NULL,
addSusieInf = TRUE,
L = 20L,
Lgreedy = 5L,
L = 10L,
Lgreedy = NULL,
coverage = 0.95,
secondaryCoverage = c(0.7, 0.5),
signalCutoff = 0.025,
Expand Down Expand Up @@ -3233,8 +3234,8 @@ setMethod(
data,
methods,
addSusieInf = TRUE,
L = 20L,
Lgreedy = 5L,
L = 10L,
Lgreedy = NULL,
coverage = 0.95,
secondaryCoverage = c(0.7, 0.5),
signalCutoff = 0.025,
Expand Down
14 changes: 7 additions & 7 deletions tests/testthat/test_fineMappingPipeline.R
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Expand Up @@ -287,11 +287,11 @@ test_that(".fmNormalizeMethods: char-vector form deduplicates + seeds susie L de
res <- pecotmr:::.fmNormalizeMethods(c("susie", "susie", "susieInf"))
expect_equal(res$tokens, c("susie", "susieInf"))
expect_equal(names(res$methodArgs), c("susie", "susieInf"))
# SuSiE-family tokens get the pipeline L / L_greedy defaults (pecotmr owns
# these, not the CLI wrappers).
expect_equal(res$methodArgs$susie$L, 20L)
expect_equal(res$methodArgs$susie$L_greedy, 5L)
expect_equal(res$methodArgs$susieInf$L, 20L)
# SuSiE-family tokens get the pipeline L default (pecotmr owns these, not the
# CLI wrappers). L_greedy defaults to NULL (greedy off), so it is left unset.
expect_equal(res$methodArgs$susie$L, 10L)
expect_null(res$methodArgs$susie$L_greedy)
expect_equal(res$methodArgs$susieInf$L, 10L)
# Non-susie-family tokens are left untouched.
expect_length(
pecotmr:::.fmNormalizeMethods("mvsusie")$methodArgs$mvsusie,
Expand All @@ -306,8 +306,8 @@ test_that(".fmNormalizeMethods: named-list keeps kwargs + fills missing susie L"
expect_equal(res$tokens, c("susie", "susieInf"))
expect_equal(res$methodArgs$susie$L, 1) # explicit kwarg wins
expect_false(res$methodArgs$susie$refine)
expect_equal(res$methodArgs$susie$L_greedy, 5L) # filled-in default
expect_equal(res$methodArgs$susieInf$L, 20L) # both filled
expect_null(res$methodArgs$susie$L_greedy) # greedy off by default (Lgreedy = NULL)
expect_equal(res$methodArgs$susieInf$L, 10L) # both filled
})

test_that(".fmNormalizeMethods: L / Lgreedy args override the susie defaults", {
Expand Down
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