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fix other susie args #595

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Merged
danielnachun merged 2 commits into from
Sep 8, 2026
Merged

fix other susie args #595

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b7d2234
fix other susie args
danielnachun Sep 5, 2026
08ab4a2
make colocPipeline more flexible
danielnachun Sep 8, 2026
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40 changes: 30 additions & 10 deletions R/ColocResult.R
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Original file line number Diff line number Diff line change
Expand Up @@ -97,6 +97,8 @@ methods::setValidity("ColocResult", function(object) {
"trait",
"method",
"gwasStudy",
"gwasContext",
"gwasTrait",
"gwasMethod",
"blockId",
"qtlCs",
Expand Down Expand Up @@ -169,8 +171,8 @@ setMethod("show", "ColocResult", function(object) {
return(invisible(NULL))
}
md <- mcols(object, use.names = FALSE)
cat(" QTL studies :", str_flatten(unique(md$study), ", "), "\n")
cat(" GWAS studies:", str_flatten(unique(md$gwasStudy), ", "), "\n")
cat(" studies :", str_flatten(unique(md$study), ", "), "\n")
cat(" paired with :", str_flatten(unique(md$gwasStudy), ", "), "\n")
cat(" variants :", sum(lengths(object)), "across all pairs\n")
cat(
" max PP.H4 :",
Expand All @@ -187,10 +189,12 @@ setMethod("show", "ColocResult", function(object) {
#' table and the per-pair variant tables that go with it. Callers normally
#' get one from \code{\link{colocPipeline}} rather than building it directly.
#' @param pairs A data frame with one row per tested pair, carrying at least
#' the identity columns (\code{study}, \code{context}, \code{trait},
#' \code{method}, \code{gwasStudy}, \code{gwasMethod}), \code{blockId},
#' \code{qtlCs}, \code{gwasCs}, \code{nSnps} and \code{PP.H0.abf} through
#' \code{PP.H4.abf}.
#' the identity columns of both sides (\code{study}, \code{context},
#' \code{trait}, \code{method} and \code{gwasStudy}, \code{gwasContext},
#' \code{gwasTrait}, \code{gwasMethod}), \code{blockId}, \code{qtlCs},
#' \code{gwasCs}, \code{nSnps} and \code{PP.H0.abf} through
#' \code{PP.H4.abf}. A GWAS side has no context or trait axis, so those two
#' columns are \code{NA} for it.
#' @param variants A list, parallel to \code{pairs}' rows, of per-pair data
#' frames with a \code{variant_id} column and a \code{SNP.PP.H4} column.
#' @param ldSketch Optional genotype panel (see \code{\link{readGenotypes}})
Expand All @@ -200,7 +204,9 @@ setMethod("show", "ColocResult", function(object) {
#' @examples
#' pairs <- data.frame(
#' study = "s1", context = "c1", trait = "g1", method = "susie",
#' gwasStudy = "G1", gwasMethod = "susie", blockId = "chr1_1_1000",
#' gwasStudy = "G1", gwasContext = NA_character_,
#' gwasTrait = NA_character_, gwasMethod = "susie",
#' blockId = "chr1_1_1000",
#' qtlCs = 1L, gwasCs = 1L, nSnps = 2L,
#' PP.H0.abf = 0.1, PP.H1.abf = 0.1, PP.H2.abf = 0.1,
#' PP.H3.abf = 0.1, PP.H4.abf = 0.6
Expand Down Expand Up @@ -301,10 +307,22 @@ ColocResult <- function(pairs, variants, ldSketch = NULL) {
# ---- views ------------------------------------------------------------------

# The columns that identify a gene-level unit: everything that is fixed within
# one QTL molecular trait tested against one GWAS study.
# one first-side trait tested against one second-side trait. Both sides carry
# the full (study, context, trait, method) tuple, since either may be a QTL
# collection whose rows differ only on context or trait -- grouping on the
# study alone would pool two distinct molecular phenotypes into one unit.
# @noRd
.crGeneCols <- function() {
c("study", "context", "trait", "method", "gwasStudy", "gwasMethod")
c(
"study",
"context",
"trait",
"method",
"gwasStudy",
"gwasContext",
"gwasTrait",
"gwasMethod"
)
}

#' @rdname colocViews
Expand Down Expand Up @@ -560,7 +578,9 @@ setMethod(
#' @examples
#' pairs <- data.frame(
#' study = "s1", context = "c1", trait = "g1", method = "susie",
#' gwasStudy = "G1", gwasMethod = "susie", blockId = "chr1_1_1000",
#' gwasStudy = "G1", gwasContext = NA_character_,
#' gwasTrait = NA_character_, gwasMethod = "susie",
#' blockId = "chr1_1_1000",
#' qtlCs = 1L, gwasCs = 1L, nSnps = 2L,
#' PP.H0.abf = 0.1, PP.H1.abf = 0.1, PP.H2.abf = 0.1,
#' PP.H3.abf = 0.1, PP.H4.abf = 0.6
Expand Down
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