add readers and writers

DESCRIPTION

@@ -174,12 +174,13 @@ Collate:
     'qtlEnrichmentPipeline.R'
     'regularizedRegressionWrappers.R'
     'relatednessQc.R'
+    'twasWeights.R'
+    'resultWriters.R'
+    'resultReaders.R'
     'sldscPostprocessingPipeline.R'
     'sldscWrapper.R'
-    'twasWeights.R'
     'twasWeightsPipeline.R'
     'twasWeightsRow.R'
-    'vcfWriter.R'
 Depends: 
     R (>= 4.5)
 LazyData: false

NAMESPACE

@@ -154,6 +154,7 @@ export(bayesCWeights)
 export(bayesLWeights)
 export(bayesNWeights)
 export(bayesRWeights)
+export(blockId)
 export(blockMetadata)
 export(buildLdEigen)
 export(buildLdScore)
@@ -210,6 +211,8 @@ export(ensembleWeights)
 export(estCtwasGroupPriors)
 export(estimateH2)
 export(estimateSparsity)
+export(exportToBed)
+export(exportToVcf)
 export(extractCsInfo)
 export(extractTopPipInfo)
 export(filterInvalidSummaryStat)
@@ -233,8 +236,10 @@ export(frqData)
 export(fsusieAffectedRegions)
 export(fsusieCredibleBand)
 export(fsusieGetCs)
+export(fsusieTraitEffects)
 export(fsusieWeights)
 export(fullFit)
+export(genomicOrder)
 export(genomicRegion)
 export(genotypeCovariates)
 export(genotypes)
@@ -343,10 +348,12 @@ export(qtlSumStatsFromZMatrix)
 export(raiss)
 export(readAfreq)
 export(readAnnotations)
+export(readFineMappingResult)
 export(readGenotypes)
 export(readSldscAnnot)
 export(readSldscFrq)
 export(readSldscTrait)
+export(readTwasWeights)
 export(refPanel)
 export(refVariantInfo)
 export(regionToDf)
@@ -409,7 +416,6 @@ export(variantInfo)
 export(waldTestPval)
 export(weightStandardized)
 export(weightsDataType)
-export(writeSumStatsVcf)
 export(xvarCutoff)
 export(z)
 exportClasses(AnnotationMatrix)
@@ -486,6 +492,7 @@ exportMethods(as.data.frame)
 exportMethods(as.list)
 exportMethods(baselineAnnotations)
 exportMethods(bindROWS)
+exportMethods(blockId)
 exportMethods(blockMetadata)
 exportMethods(coef)
 exportMethods(colnames)
@@ -507,11 +514,14 @@ exportMethods(cvResult)
 exportMethods(eigenList)
 exportMethods(endoapply)
 exportMethods(estimateH2)
+exportMethods(exportToBed)
+exportMethods(exportToVcf)
 exportMethods(fineMappingPipeline)
 exportMethods(fineMappingResult)
 exportMethods(frqData)
 exportMethods(fsusieAffectedRegions)
 exportMethods(fsusieCredibleBand)
+exportMethods(fsusieTraitEffects)
 exportMethods(fullFit)
 exportMethods(genomicRegion)
 exportMethods(genotypeCovariates)
@@ -590,7 +600,6 @@ exportMethods(variantInfo)
 exportMethods(weightStandardized)
 exportMethods(weights)
 exportMethods(weightsDataType)
-exportMethods(writeSumStatsVcf)
 exportMethods(xvarCutoff)
 exportMethods(z)
 importClassesFrom(GenomicRanges,GRanges)
@@ -623,6 +632,7 @@ importFrom(GenomicRanges,
   start
 )
 importFrom(IRanges,
+  CharacterList,
   DataFrameList,
   IRanges,
   findOverlaps
@@ -632,7 +642,9 @@ importFrom(MultiAssayExperiment,longForm)
 importFrom(Rsamtools,
   TabixFile,
   asBcf,
+  bgzip,
   headerTabix,
+  indexTabix,
   scanTabix,
   seqnamesTabix
 )

R/AllClasses.R

@@ -772,6 +772,7 @@ setMethod("methodNames", "FineMappingResultBase", function(x) {
     unique(as.character(x$method))
 })
 
+
 #' @noRd
 setMethod(
     "adjustPips",
@@ -1085,6 +1086,24 @@ setMethod("fsusieCredibleBand", "FineMappingResultBase", function(x) {
     .fmrAggregateView(x, perEntry = .fmrRowFsusieCredibleBand)
 })
 
+#' @rdname fsusieTraitEffects
+#' @export
+setMethod("fsusieTraitEffects", "FineMappingResultBase", function(x) {
+    # Not .fmrAggregateView(): the per-entry payload carries only the fit, and
+    # this view also needs the row's `jointTraits` column for the trait names.
+    meta <- .fmrRowMetadata(x)
+    parts <- compact(map(
+        seq_len(nrow(x)),
+        .fsusieEntryTraitEffects,
+        x = x,
+        meta = meta
+    ))
+    if (length(parts) == 0L) {
+        return(bind_cols(slice(meta, integer(0)), .emptyTraitEffects()))
+    }
+    .rbindAligned(parts)
+})
+
 #' @rdname fsusieAffectedRegions
 #' @export
 setMethod("fsusieAffectedRegions", "FineMappingResultBase", function(x) {