fix CV issues

DESCRIPTION

@@ -93,8 +93,10 @@ Collate:
     'GenotypeHandle.R'
     'AllClasses.R'
     'AnnotationMatrix.R'
-    'FineMappingEntry.R'
     'tupleSelectors.R'
+    'CtwasResult.R'
+    'CtwasResultEntry.R'
+    'FineMappingEntry.R'
     'GwasFineMappingResult.R'
     'H2Estimate.R'
     'JointGroup.R'
@@ -113,6 +115,7 @@ Collate:
     'colocPipeline.R'
     'colocboostPipeline.R'
     'cpp11.R'
+    'crossValidation.R'
     'ctwasPipeline.R'
     'deprecated.R'
     'exampleData.R'

NAMESPACE

@@ -7,6 +7,8 @@ S3method(postprocessFinemappingFit,susie)
 S3method(postprocessFinemappingFit,susieInf)
 S3method(postprocessFinemappingFit,susieRss)
 export(AnnotationMatrix)
+export(CtwasResult)
+export(CtwasResultEntry)
 export(FineMappingEntry)
 export(GenotypeHandle)
 export(GwasFineMappingResult)
@@ -23,6 +25,8 @@ export(TwasWeightsEntry)
 export(adjustPips)
 export(alignVariantNames)
 export(alleleQc)
+export(asCtwasResult)
+export(asGranges)
 export(assembleCtwasInputs)
 export(autoDecision)
 export(bLassoWeights)
@@ -43,7 +47,9 @@ export(colocPipeline)
 export(colocPostProcessor)
 export(colocWrapper)
 export(colocboostPipeline)
+export(combineFineMappingResults)
 export(combinePValues)
+export(combineTwasWeights)
 export(computeBlockLdCor)
 export(computeCoefficientsGlasso)
 export(computeCovDiag)
@@ -99,12 +105,14 @@ export(getContexts)
 export(getCorrelation)
 export(getCs)
 export(getCtwasMetaData)
+export(getCtwasParam)
 export(getCvFits)
 export(getCvResult)
 export(getDataType)
 export(getEigenList)
 export(getEnrichment)
 export(getFineMappingResult)
+export(getFinemap)
 export(getFits)
 export(getFormat)
 export(getFrqData)
@@ -138,6 +146,7 @@ export(getQcInfo)
 export(getQtlDatasets)
 export(getRefPanel)
 export(getRefVariantInfo)
+export(getRegion)
 export(getResidualizedGenotypes)
 export(getResidualizedPhenotypes)
 export(getSampleIds)
@@ -150,6 +159,7 @@ export(getStandardized)
 export(getStudy)
 export(getSumStats)
 export(getSumstatDf)
+export(getSusieAlpha)
 export(getSusieFit)
 export(getSusieResult)
 export(getTauBlocks)
@@ -233,6 +243,7 @@ export(prsCs)
 export(prsCsWeights)
 export(qtlEnrichment)
 export(qtlEnrichmentPipeline)
+export(qtlSumStatsFromZMatrix)
 export(raiss)
 export(readAfreq)
 export(readAnnotations)
@@ -244,6 +255,7 @@ export(regionDataToIndInput)
 export(regionDataToRssInput)
 export(regionToDf)
 export(regionsOverlap)
+export(resolveWeights)
 export(rssAnalysisPipeline)
 export(sanitizeMashData)
 export(scadRssWeights)
@@ -253,6 +265,7 @@ export(sdpr)
 export(sdprWeights)
 export(slalom)
 export(sldscPostprocessingPipeline)
+export(sldscSubsetMeta)
 export(sliceMashData)
 export(standardiseSumstatsColumns)
 export(standardizeSldscTrait)
@@ -304,12 +317,14 @@ exportMethods(getBlocks)
 exportMethods(getContexts)
 exportMethods(getCorrelation)
 exportMethods(getCs)
+exportMethods(getCtwasParam)
 exportMethods(getCvFits)
 exportMethods(getCvResult)
 exportMethods(getDataType)
 exportMethods(getEigenList)
 exportMethods(getEnrichment)
 exportMethods(getFineMappingResult)
+exportMethods(getFinemap)
 exportMethods(getFits)
 exportMethods(getFormat)
 exportMethods(getFrqData)
@@ -342,6 +357,7 @@ exportMethods(getQcDiagnostics)
 exportMethods(getQcInfo)
 exportMethods(getQtlDatasets)
 exportMethods(getRefPanel)
+exportMethods(getRegion)
 exportMethods(getResidualizedGenotypes)
 exportMethods(getResidualizedPhenotypes)
 exportMethods(getSampleIds)
@@ -354,6 +370,7 @@ exportMethods(getStandardized)
 exportMethods(getStudy)
 exportMethods(getSumStats)
 exportMethods(getSumstatDf)
+exportMethods(getSusieAlpha)
 exportMethods(getSusieFit)
 exportMethods(getTauBlocks)
 exportMethods(getTopLoci)
@@ -371,6 +388,7 @@ exportMethods(hasGenotypes)
 exportMethods(nSnps)
 exportMethods(readAnnotations)
 exportMethods(readGenotypes)
+exportMethods(resolveWeights)
 exportMethods(show)
 exportMethods(subsetChr)
 exportMethods(twasWeightsPipeline)
@@ -444,6 +462,7 @@ importFrom(stats,complete.cases)
 importFrom(stats,cor)
 importFrom(stats,cutree)
 importFrom(stats,hclust)
+importFrom(stats,lm)
 importFrom(stats,median)
 importFrom(stats,na.omit)
 importFrom(stats,optim)

R/AllClasses.R

@@ -178,9 +178,12 @@ setGeneric(".fmrSelectEntry", function(x, ...) standardGeneric(".fmrSelectEntry"
 setMethod("getCs", "FineMappingResultBase",
   function(x, study = NULL, context = NULL, trait = NULL, method = NULL,
            region = NULL, coverage = 0.95, ...) {
-    getCs(.fmrSelectEntry(x, study = study, context = context, trait = trait,
-                          method = method, region = region),
-          coverage = coverage)
+    # Selectors pinning one entry -> that entry's bare credible-set table; no /
+    # partial selectors -> aggregate every matching entry's credible sets,
+    # prefixed with the row identity (study/context/trait/region_id/method).
+    .fmrAggregateView(x, study = study, context = context, trait = trait,
+      method = method, region = region,
+      perEntry = function(e) getCs(e, coverage = coverage))
   })
 
 #' @rdname getTopLoci
@@ -189,9 +192,27 @@ setMethod("getTopLoci", "FineMappingResultBase",
   function(x, type = c("data.frame", "GRanges"), signalCutoff = 0.025,
            study = NULL, context = NULL, trait = NULL, method = NULL,
            region = NULL, ...) {
-    getTopLoci(.fmrSelectEntry(x, study = study, context = context,
-                               trait = trait, method = method, region = region),
-               type = match.arg(type), signalCutoff = signalCutoff)
+    type <- match.arg(type)
+    # type = "GRanges" can only be honored for a single pinned entry; the
+    # aggregate (identity-prefixed) form is data.frame-only.
+    if (type == "GRanges") {
+      sel <- tryCatch(
+        .fmrSelectEntry(x, study = study, context = context, trait = trait,
+                        method = method, region = region),
+        error = function(e) e)
+      if (inherits(sel, "error")) {
+        stop("getTopLoci: aggregating across multiple entries requires ",
+             "type = 'data.frame'.")
+      }
+      return(getTopLoci(sel, type = "GRanges", signalCutoff = signalCutoff))
+    }
+    # data.frame: bare per-variant table when selectors pin one entry, else the
+    # per-variant tables of every matching row stacked with row identity
+    # (study / context / trait / region_id / method) columns.
+    .fmrAggregateView(x, study = study, context = context, trait = trait,
+      method = method, region = region,
+      perEntry = function(e) getTopLoci(e, type = "data.frame",
+                                        signalCutoff = signalCutoff))
   })
 
 #' @rdname getMarginalEffects
@@ -200,11 +221,18 @@ setMethod("getMarginalEffects", "FineMappingResultBase",
   function(x, maxPval = NULL,
            study = NULL, context = NULL, trait = NULL, method = NULL,
            region = NULL, ...) {
-    getMarginalEffects(.fmrSelectEntry(x, study = study, context = context,
-                                       trait = trait, method = method,
-                                       region = region), maxPval = maxPval)
+    # Selectors pinning one entry -> that entry's bare marginal table; no /
+    # partial selectors -> aggregate every matching entry's marginals, prefixed
+    # with the row identity (study/context/trait/region_id/method).
+    .fmrAggregateView(x, study = study, context = context, trait = trait,
+      method = method, region = region,
+      perEntry = function(e) getMarginalEffects(e, maxPval = maxPval))
   })
 
+#' @rdname getRegion
+#' @export
+setMethod("getRegion", "FineMappingResultBase", function(x, ...) .getRegionColumn(x))
+
 #' @rdname getSusieFit
 #' @export
 setMethod("getSusieFit", "FineMappingResultBase",

R/AllGenerics.R

@@ -486,6 +486,50 @@ setGeneric("getCs", function(x, ...) standardGeneric("getCs"))
 #' @export
 setGeneric("getWeights", function(x, ...) standardGeneric("getWeights"))
 
+#' @title Resolve Per-Variant Weights From a Weight Source
+#' @description Return an aligned \code{(variantIds, weights)} pair from a single
+#'   weight-source entry, so cTWAS and \code{\link{causalInferencePipeline}}
+#'   extract weights identically whether the source is a
+#'   \code{TwasWeightsEntry} (its learned weight vector) or a
+#'   \code{FineMappingEntry} (its topLoci posterior effect).
+#' @param x A \code{TwasWeightsEntry} or \code{FineMappingEntry}.
+#' @param ... Reserved for future use.
+#' @return A \code{list} with \code{variantIds} (character) and \code{weights}
+#'   (numeric) of equal length; both empty when no usable weights are present.
+#' @export
+setGeneric("resolveWeights", function(x, ...) standardGeneric("resolveWeights"))
+
+#' @title Get cTWAS Fine-mapping Posteriors
+#' @description Return the per-gene (and per-SNP) fine-mapping posterior table
+#'   from a \code{\link{CtwasResultEntry}} or a \code{\link{CtwasResult}}
+#'   collection (aggregated across rows, tagged with run identity).
+#' @param x A \code{CtwasResultEntry} or \code{CtwasResult}.
+#' @param ... Class-specific selection arguments.
+#' @return A \code{data.frame} of posteriors (or \code{NULL} when absent).
+#' @export
+setGeneric("getFinemap", function(x, ...) standardGeneric("getFinemap"))
+
+#' @title Get cTWAS Per-effect Susie Alpha Table
+#' @description Return the full per-effect susie alpha table
+#'   (\code{ctwas::finemap_regions} \code{susie_alpha_res} shape) from a
+#'   \code{\link{CtwasResultEntry}} or a \code{\link{CtwasResult}} collection
+#'   (aggregated across rows, tagged with run identity). This is the fuller
+#'   cTWAS output retained so the raw run is reconstructable.
+#' @param x A \code{CtwasResultEntry} or \code{CtwasResult}.
+#' @param ... Class-specific selection arguments.
+#' @return A \code{data.frame} of per-effect alphas (or \code{NULL} when absent).
+#' @export
+setGeneric("getSusieAlpha", function(x, ...) standardGeneric("getSusieAlpha"))
+
+#' @title Get cTWAS Group Prior Parameters
+#' @description Return the estimated \code{group_prior} / \code{group_prior_var}
+#'   of a \code{\link{CtwasResultEntry}}.
+#' @param x A \code{CtwasResultEntry}.
+#' @param ... Reserved for future use.
+#' @return The stored parameter object (typically a list), or \code{NULL}.
+#' @export
+setGeneric("getCtwasParam", function(x, ...) standardGeneric("getCtwasParam"))
+
 #' @title Get Standardized Flag
 #' @description Check whether weights are on the standardized scale.
 #' @param x A \code{TwasWeightsEntry} or \code{TwasWeights}.
@@ -591,6 +635,18 @@ setGeneric("getContexts", function(x) standardGeneric("getContexts"))
 #' @export
 setGeneric("getTraits", function(x) standardGeneric("getTraits"))
 
+#' @title Get Per-Row Genomic Regions
+#' @description Return the genomic anchor of each row of a per-tuple collection
+#'   as a \code{GRanges} with one range per row -- the trait's own region for a
+#'   \code{TwasWeights}, or the fine-mapping window for a \code{FineMappingResult}.
+#'   This is location provenance (e.g. for cTWAS LD-block placement).
+#' @param x The object.
+#' @param ... Reserved for future use.
+#' @return A \code{GRanges} with one range per row of \code{x}, or an empty
+#'   \code{GRanges} when the collection carries no region provenance.
+#' @export
+setGeneric("getRegion", function(x, ...) standardGeneric("getRegion"))
+
 #' @title Get Residualized Genotypes
 #' @description Residualize the genotype matrix against the per-context
 #'   phenotype covariates and the genotype covariates, optionally