StatFunGen · danielnachun · Aug 5, 2026 · Aug 5, 2026
diff --git a/NAMESPACE b/NAMESPACE
@@ -6,8 +6,6 @@ S3method(postprocessFinemappingFit,susiF)
 S3method(postprocessFinemappingFit,susie)
 S3method(postprocessFinemappingFit,susieInf)
 S3method(postprocessFinemappingFit,susieRss)
-export(.fullFitColumns)
-export(.overlapPrefixNonKey)
 export(AnnotationMatrix)
 export(CtwasResult)
 export(CtwasResultEntry)
@@ -41,6 +39,7 @@ export(bayesLWeights)
 export(bayesNWeights)
 export(bayesRWeights)
 export(buildMrmashPriorMatrices)
+export(buildTopLoci)
 export(calculateFeatureScores)
 export(causalInferencePipeline)
 export(checkLd)
@@ -255,6 +254,7 @@ export(mvsusieWeights)
 export(nSignificantScore)
 export(nSnps)
 export(normalizeVariantId)
+export(overlapTopLoci)
 export(parseCsCorr)
 export(parseRegion)
 export(parseVariantId)

diff --git a/R/fineMappingWrappers.R b/R/fineMappingWrappers.R
@@ -539,53 +539,6 @@ computeCsTable <- function(fit, dataX, coverage, csInput = c("X", "Xcorr", "fsus
   out
 }
 
-#' Build the unified top-loci table for one fit and one method.
-#'
-#' Returns the per-fit, per-method contribution to the unified \code{top_loci}
-#' table in the fixed 22-column shape. \code{postprocessFinemappingFits()}
-#' calls this once per method per fit and row-binds the results into the
-#' single \code{top_loci} returned by \code{formatFinemappingOutput()}.
-#'
-#' Output columns, in order: \code{#chr}, \code{start}, \code{end}, \code{a1},
-#' \code{a2}, \code{variant}, \code{gene}, \code{event}, \code{n}, \code{af},
-#' \code{beta}, \code{se}, \code{pip}, \code{posterior_effect_mean},
-#' \code{posterior_effect_se}, \code{cs_95}, \code{cs_70}, \code{cs_50},
-#' \code{cs_95_purity}, \code{method}, \code{grange_start}, \code{grange_end}.
-#'
-#' \code{cs_95} / \code{cs_70} / \code{cs_50} are character strings of the
-#' form \code{"<method>_<cs_index>"} where each method numbers credible sets
-#' independently from 1. Variants retained by the PIP cutoff but not in any
-#' credible set at a coverage carry \code{"<method>_0"}. \code{cs_95_purity}
-#' is the 0.95-coverage purity for the row's \code{(method, cs_95)}; rows
-#' whose \code{cs_95} is \code{"<method>_0"} carry \code{0}.
-#'
-#' Row uniqueness is \code{(variant, gene, cs_membership)} at the given
-#' \code{method}; overlapping CS within the same method produces one row per
-#' CS.
-#'
-#' @param fit Fitted SuSiE-family object (must expose \code{alpha},
-#'   \code{mu}, \code{mu2}, \code{pip}).
-#' @param csTables List of CS tables (one per coverage) from
-#'   \code{computeCsTables()}.
-#' @param variantNames Character vector of variant IDs
-#'   (\code{chr:pos:A2:A1}).
-#' @param sumstats Optional marginal-association summary (\code{betahat},
-#'   \code{sebetahat}) filling \code{beta} / \code{se}.
-#' @param af Optional numeric vector of effect-allele frequencies (frequency of
-#'   the final effect allele / \code{a1} after allele harmonization against the
-#'   LD/reference variants). Exported directly as the \code{af} column. MAF is
-#'   never exported; derive it from \code{af} at filter time. Default NULL ->
-#'   \code{af = NA_real_}.
-#' @param method Method name (e.g. \code{"susie"}, \code{"susieInf"}). Required.
-#' @param signalCutoff PIP cutoff for retaining PIP-only (non-CS) variants.
-#' @param dataX Optional regional genotype matrix.
-#' @param dataY Optional regional phenotype matrix; \code{nrow(dataY)} fills
-#'   \code{n}, \code{colnames(dataY)[1]} fills \code{gene}.
-#' @param otherQuantities Optional list. Default is NULL.
-#' @param region Optional \code{"chr:start-end"} string. Default is NULL.
-#' @return A data frame in the fixed 22-column shape for this fit and method,
-#'   or an empty data frame if nothing is retained.
-#' @export
 # Per-effect (per credible set) variant-level columns from the susie fit. Always
 # returns `within_cs_pip` (the variant's alpha in the single effect of its
 # assigned primary-coverage CS; NA for non-CS variants -- alpha is a probability,
@@ -678,6 +631,53 @@ computeCsTable <- function(fit, dataX, coverage, csInput = c("X", "Xcorr", "fsus
   }, numeric(1))
 }
 
+#' Build the unified top-loci table for one fit and one method.
+#'
+#' Returns the per-fit, per-method contribution to the unified \code{top_loci}
+#' table in the fixed 22-column shape. \code{postprocessFinemappingFits()}
+#' calls this once per method per fit and row-binds the results into the
+#' single \code{top_loci} returned by \code{formatFinemappingOutput()}.
+#'
+#' Output columns, in order: \code{#chr}, \code{start}, \code{end}, \code{a1},
+#' \code{a2}, \code{variant}, \code{gene}, \code{event}, \code{n}, \code{af},
+#' \code{beta}, \code{se}, \code{pip}, \code{posterior_effect_mean},
+#' \code{posterior_effect_se}, \code{cs_95}, \code{cs_70}, \code{cs_50},
+#' \code{cs_95_purity}, \code{method}, \code{grange_start}, \code{grange_end}.
+#'
+#' \code{cs_95} / \code{cs_70} / \code{cs_50} are character strings of the
+#' form \code{"<method>_<cs_index>"} where each method numbers credible sets
+#' independently from 1. Variants retained by the PIP cutoff but not in any
+#' credible set at a coverage carry \code{"<method>_0"}. \code{cs_95_purity}
+#' is the 0.95-coverage purity for the row's \code{(method, cs_95)}; rows
+#' whose \code{cs_95} is \code{"<method>_0"} carry \code{0}.
+#'
+#' Row uniqueness is \code{(variant, gene, cs_membership)} at the given
+#' \code{method}; overlapping CS within the same method produces one row per
+#' CS.
+#'
+#' @param fit Fitted SuSiE-family object (must expose \code{alpha},
+#'   \code{mu}, \code{mu2}, \code{pip}).
+#' @param csTables List of CS tables (one per coverage) from
+#'   \code{computeCsTables()}.
+#' @param variantNames Character vector of variant IDs
+#'   (\code{chr:pos:A2:A1}).
+#' @param sumstats Optional marginal-association summary (\code{betahat},
+#'   \code{sebetahat}) filling \code{beta} / \code{se}.
+#' @param af Optional numeric vector of effect-allele frequencies (frequency of
+#'   the final effect allele / \code{a1} after allele harmonization against the
+#'   LD/reference variants). Exported directly as the \code{af} column. MAF is
+#'   never exported; derive it from \code{af} at filter time. Default NULL ->
+#'   \code{af = NA_real_}.
+#' @param method Method name (e.g. \code{"susie"}, \code{"susieInf"}). Required.
+#' @param signalCutoff PIP cutoff for retaining PIP-only (non-CS) variants.
+#' @param dataX Optional regional genotype matrix.
+#' @param dataY Optional regional phenotype matrix; \code{nrow(dataY)} fills
+#'   \code{n}, \code{colnames(dataY)[1]} fills \code{gene}.
+#' @param otherQuantities Optional list. Default is NULL.
+#' @param region Optional \code{"chr:start-end"} string. Default is NULL.
+#' @return A data frame in the fixed 22-column shape for this fit and method,
+#'   or an empty data frame if nothing is retained.
+#' @export
 buildTopLoci <- function(fit, csTables, variantNames, sumstats = NULL,
                          af = NULL, method, signalCutoff = 0,
                          dataX = NULL, dataY = NULL,

diff --git a/R/overlapTopLoci.R b/R/overlapTopLoci.R
@@ -1,29 +1,3 @@
-#' Overlap QTL and GWAS top loci by allele-aware variant matching
-#'
-#' Intersect the top-loci tables of a \code{QtlFineMappingResult} and a
-#' \code{GwasFineMappingResult} on shared variants, matched with pecotmr's
-#' allele-aware \code{\link{matchVariants}} (handling strand flips / ref-alt
-#' swaps rather than naive id equality). The GWAS side is harmonized to the QTL
-#' orientation: its signed effect columns (\code{beta}, \code{z},
-#' \code{conditional_effect}) are sign-flipped and its effect-allele frequency
-#' (\code{af}) is complemented wherever a swap occurred. The result keeps the
-#' variant key columns once (from the QTL, the reference orientation) and
-#' prefixes every other column \code{qtl_} / \code{gwas_}. A variant shared
-#' across several QTL contexts and/or GWAS studies yields one row per
-#' (QTL entry x GWAS entry) pair (a wide cross-product per variant).
-#'
-#' @param qtl A \code{QtlFineMappingResult}.
-#' @param gwas A \code{GwasFineMappingResult}.
-#' @param signalCutoff PIP cutoff forwarded to \code{\link{getTopLoci}} for both
-#'   inputs. Default 0.025.
-#' @param type \code{"data.frame"} (default) or \code{"GRanges"}.
-#' @param ... Ignored.
-#' @return A \code{data.frame} (or \code{GRanges}) keyed on the QTL variant
-#'   (\code{variant_id, chrom, pos, A1, A2}) with all other columns prefixed
-#'   \code{qtl_} / \code{gwas_}. Zero rows when there is no allele-aware overlap.
-#' @seealso \code{\link{getTopLoci}}, \code{\link{matchVariants}}
-#' @include AllGenerics.R AllClasses.R QtlFineMappingResult.R GwasFineMappingResult.R
-#' @export
 # Prefix a top-loci frame's NON-key columns with `pfx` (key columns unchanged).
 # @noRd
 .overlapPrefixNonKey <- function(df, pfx, keyCols)
@@ -50,6 +24,32 @@
 # @noRd
 .overlapFinish <- function(df, type) if (type == "GRanges") .overlapToGRanges(df) else df
 
+#' Overlap QTL and GWAS top loci by allele-aware variant matching
+#'
+#' Intersect the top-loci tables of a \code{QtlFineMappingResult} and a
+#' \code{GwasFineMappingResult} on shared variants, matched with pecotmr's
+#' allele-aware \code{\link{matchVariants}} (handling strand flips / ref-alt
+#' swaps rather than naive id equality). The GWAS side is harmonized to the QTL
+#' orientation: its signed effect columns (\code{beta}, \code{z},
+#' \code{conditional_effect}) are sign-flipped and its effect-allele frequency
+#' (\code{af}) is complemented wherever a swap occurred. The result keeps the
+#' variant key columns once (from the QTL, the reference orientation) and
+#' prefixes every other column \code{qtl_} / \code{gwas_}. A variant shared
+#' across several QTL contexts and/or GWAS studies yields one row per
+#' (QTL entry x GWAS entry) pair (a wide cross-product per variant).
+#'
+#' @param qtl A \code{QtlFineMappingResult}.
+#' @param gwas A \code{GwasFineMappingResult}.
+#' @param signalCutoff PIP cutoff forwarded to \code{\link{getTopLoci}} for both
+#'   inputs. Default 0.025.
+#' @param type \code{"data.frame"} (default) or \code{"GRanges"}.
+#' @param ... Ignored.
+#' @return A \code{data.frame} (or \code{GRanges}) keyed on the QTL variant
+#'   (\code{variant_id, chrom, pos, A1, A2}) with all other columns prefixed
+#'   \code{qtl_} / \code{gwas_}. Zero rows when there is no allele-aware overlap.
+#' @seealso \code{\link{getTopLoci}}, \code{\link{matchVariants}}
+#' @include AllGenerics.R AllClasses.R QtlFineMappingResult.R GwasFineMappingResult.R
+#' @export
 setGeneric("overlapTopLoci",
   function(qtl, gwas, ...) standardGeneric("overlapTopLoci"))
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -213,7 +213,7 @@ reference:
       - getMaf
       - getN
       - getP
-      - getSE
+      - getSe
       - getSumStats
       - getSumstatDf
       - getVarY
@@ -389,6 +389,7 @@ reference:
       - enforceDesignFullRank
       - ldClumpByScore
       - ldLoader
+      - loadLdBlock
       - ldPruneByCorrelation
       - filterVariantsByLdReference
 
@@ -620,7 +621,7 @@ reference:
       # Implementation details with .Rd topics but no front-facing role.
       - as.data.frame.GwasSumStats
       - rescaleCovW0
-      - ".fullFitColumns"
+      - buildTopLoci
       - "getSumStats,GwasSumStats-method"
 
 footer:

diff --git a/man/dot-fullFitColumns.Rd → man/buildTopLoci.Rd b/man/dot-fullFitColumns.Rd → man/buildTopLoci.Rd
diff --git a/man/dot-overlapPrefixNonKey.Rd → man/overlapTopLoci.Rd b/man/dot-overlapPrefixNonKey.Rd → man/overlapTopLoci.Rd