add mashr and fsusie fixes

.github/recipe/recipe.yaml

@@ -24,7 +24,6 @@ requirements:
     - ${{ compiler('cxx') }}
   host:
     - bioconductor-biocparallel
-    - bioconductor-biostrings
     - bioconductor-genomicranges
     - bioconductor-iranges
     - bioconductor-qvalue
@@ -43,6 +42,7 @@ requirements:
     - r-coda
     - r-coloc
     - r-colocboost
+    - r-corshrink
     - r-cpp11
     - r-cpp11armadillo
     - r-ctwas
@@ -59,6 +59,7 @@ requirements:
     - r-mashr
     - r-matrix
     - r-matrixstats
+    - r-metafor
     - r-mr.ash.alpha
     - r-mr.mashr
     - r-mvsusier
@@ -81,6 +82,7 @@ requirements:
     - r-tibble
     - r-tictoc
     - r-tidyr
+    - r-udr
     - r-vctrs
     - r-vroom
     - r-xgboost
@@ -105,6 +107,7 @@ requirements:
     - r-coda
     - r-coloc
     - r-colocboost
+    - r-corshrink
     - r-cpp11
     - r-cpp11armadillo
     - r-ctwas
@@ -121,6 +124,7 @@ requirements:
     - r-mashr
     - r-matrix
     - r-matrixstats
+    - r-metafor
     - r-mr.ash.alpha
     - r-mr.mashr
     - r-mvsusier
@@ -143,6 +147,7 @@ requirements:
     - r-tibble
     - r-tictoc
     - r-tidyr
+    - r-udr
     - r-vctrs
     - r-vroom
     - r-xgboost

.gitignore

@@ -2,7 +2,6 @@ src/*.o
 src/*.gcda
 src/*.so
 src/*.dylib
-src/Makevars
 **/.ipynb_checkpoints
 .Rproj.user
 **/.DS_Store

DESCRIPTION

@@ -28,6 +28,7 @@ Imports:
     dplyr,
     magrittr,
     matrixStats,
+    metafor,
     methods,
     purrr,
     quadprog,
@@ -48,6 +49,8 @@ Suggests:
     bigsnpr,
     bigstatsr,
     coda,
+    CorShrink,
+    ctwas,
     flashier,
     fsusieR,
     GBJ,
@@ -57,7 +60,6 @@ Suggests:
     igraph,
     knitr,
     L0Learn,
-    lassosum,
     mashr,
     mr.mashr,
     mvsusieR,
@@ -76,18 +78,21 @@ Suggests:
     SNPRelate,
     snpStats,
     testthat,
+    udr,
     VariantAnnotation
 Remotes:
+    kkdey/CorShrink,
     stephenslab/fsusieR,
     stephenslab/mvsusieR,
     stephenslab/susieR,
+    stephenslab/udr,
+    xinhe-lab/multigroup_ctwas,
 LinkingTo:
     cpp11,
     cpp11armadillo
 NeedsCompilation: yes
 VignetteBuilder: knitr
 Config/roxygen2/version: 8.0.0
-RoxygenNote: 7.3.3
 Collate:
     'AllGenerics.R'
     'GenotypeHandle.R'
@@ -113,28 +118,33 @@ Collate:
     'TwasWeightsEntry.R'
     'causalInferencePipeline.R'
     'colocPipeline.R'
+    'qtlSumStats.R'
     'colocboostPipeline.R'
     'cpp11.R'
+    'credibleSetSummary.R'
     'crossValidation.R'
     'ctwasPipeline.R'
     'deprecated.R'
     'exampleData.R'
+    'gwasSumStats.R'
     'fineMappingPipeline.R'
     'fineMappingWrappers.R'
+    'fsusieAccessors.R'
     'genotypeIo.R'
-    'gwasSumStats.R'
+    'getLbf.R'
     'h2Annotations.R'
     'h2EstimationWrappers.R'
     'jointEngine.R'
     'jointSpecification.R'
     'ld.R'
     'sumstatsQc.R'
     'variantId.R'
-    'qtlSumStats.R'
     'manifestLoaders.R'
     'mashPipeline.R'
     'mashWrapper.R'
+    'overlapTopLoci.R'
     'pvalCombine.R'
+    'qtlAssociationPostprocess.R'
     'qtlEnrichmentPipeline.R'
     'regularizedRegressionWrappers.R'
     'relatednessQc.R'

NAMESPACE

@@ -6,6 +6,7 @@ S3method(postprocessFinemappingFit,susiF)
 S3method(postprocessFinemappingFit,susie)
 S3method(postprocessFinemappingFit,susieInf)
 S3method(postprocessFinemappingFit,susieRss)
+export(.fullFitColumns)
 export(AnnotationMatrix)
 export(CtwasResult)
 export(CtwasResultEntry)
@@ -39,7 +40,7 @@ export(bayesLWeights)
 export(bayesNWeights)
 export(bayesRWeights)
 export(buildMrmashPriorMatrices)
-export(buildTopLoci)
+export(calculateFeatureScores)
 export(causalInferencePipeline)
 export(checkLd)
 export(classifyVariantType)
@@ -89,6 +90,8 @@ export(fitMvsusie)
 export(fitMvsusieRss)
 export(fitSusieInfThenSusieRss)
 export(formatFinemappingOutput)
+export(fsusieAffectedRegions)
+export(fsusieCredibleBand)
 export(fsusieGetCs)
 export(fsusieWeights)
 export(fsusieWrapper)
@@ -98,11 +101,13 @@ export(getAnnotData)
 export(getAnnotationMeta)
 export(getAnnotations)
 export(getBaseline)
+export(getBeta)
 export(getBlockMetadata)
 export(getBlocks)
 export(getCandidates)
 export(getContexts)
 export(getCorrelation)
+export(getCredibleSetSummary)
 export(getCs)
 export(getCtwasMetaData)
 export(getCtwasParam)
@@ -123,6 +128,7 @@ export(getGenotypeHandle)
 export(getGenotypes)
 export(getH2)
 export(getInSample)
+export(getLbf)
 export(getLdBlocks)
 export(getLdMatrixList)
 export(getLdScoreWeights)
@@ -136,6 +142,7 @@ export(getMixtureWeights)
 export(getN)
 export(getNRef)
 export(getNSamples)
+export(getP)
 export(getPath)
 export(getPgenPtr)
 export(getPhenotypeCovariates)
@@ -149,9 +156,11 @@ export(getRefVariantInfo)
 export(getRegion)
 export(getResidualizedGenotypes)
 export(getResidualizedPhenotypes)
+export(getSE)
 export(getSampleIds)
 export(getScaleResiduals)
 export(getScoreStats)
+export(getSignificantQtls)
 export(getSnpIdx)
 export(getSnpInfo)
 export(getSnpRanges)
@@ -165,6 +174,7 @@ export(getSusieResult)
 export(getTauBlocks)
 export(getTopLoci)
 export(getTraitNames)
+export(getTraitPosition)
 export(getTraitRun)
 export(getTraitRuns)
 export(getTraits)
@@ -213,16 +223,23 @@ export(loadStudyLd)
 export(loadTsvRegion)
 export(loadTwasWeights)
 export(makePairwiseContrastCol)
+export(mashCovarianceComponents)
+export(mashInput)
+export(mashModelFit)
 export(mashPipeline)
+export(mashPosterior)
+export(mashPosteriorContrast)
+export(mashPriorCovariances)
 export(mashRandNullSample)
+export(mashResidualCorrelation)
 export(matchRefPanel)
 export(mcpRssWeights)
 export(mcpWeights)
 export(mergeCtwasBoundaryRegions)
 export(mergeMashData)
 export(mergeSusieCs)
 export(mergeVariantInfo)
-export(metaAnalysisPerCell)
+export(metaAnalysisPerCondition)
 export(metaSldscRandom)
 export(mrAshRssWeights)
 export(mrashWeights)
@@ -232,17 +249,21 @@ export(mrmashWrapper)
 export(multivariateAnalysisPipeline)
 export(mvsusieRssWeights)
 export(mvsusieWeights)
+export(nSignificantScore)
 export(nSnps)
 export(normalizeVariantId)
+export(overlapTopLoci)
 export(parseCsCorr)
 export(parseRegion)
 export(parseVariantId)
 export(penalizedRss)
 export(postprocessFinemappingFits)
 export(prsCs)
 export(prsCsWeights)
+export(qtlAssociationPostprocess)
 export(qtlEnrichment)
 export(qtlEnrichmentPipeline)
+export(qtlSumStatsFromBetaMatrix)
 export(qtlSumStatsFromZMatrix)
 export(raiss)
 export(readAfreq)
@@ -260,6 +281,7 @@ export(rssAnalysisPipeline)
 export(sanitizeMashData)
 export(scadRssWeights)
 export(scadWeights)
+export(scoreFromCs)
 export(screenCtwasRegions)
 export(sdpr)
 export(sdprWeights)
@@ -307,15 +329,19 @@ exportMethods(colocboostPipeline)
 exportMethods(computeLdScores)
 exportMethods(estimateH2)
 exportMethods(fineMappingPipeline)
+exportMethods(fsusieAffectedRegions)
+exportMethods(fsusieCredibleBand)
 exportMethods(getAf)
 exportMethods(getAnnotCols)
 exportMethods(getAnnotData)
 exportMethods(getAnnotationMeta)
 exportMethods(getAnnotations)
+exportMethods(getBeta)
 exportMethods(getBlockMetadata)
 exportMethods(getBlocks)
 exportMethods(getContexts)
 exportMethods(getCorrelation)
+exportMethods(getCredibleSetSummary)
 exportMethods(getCs)
 exportMethods(getCtwasParam)
 exportMethods(getCvFits)
@@ -335,6 +361,7 @@ exportMethods(getGenotypeHandle)
 exportMethods(getGenotypes)
 exportMethods(getH2)
 exportMethods(getInSample)
+exportMethods(getLbf)
 exportMethods(getLdBlocks)
 exportMethods(getLdMatrixList)
 exportMethods(getLdScoreWeights)
@@ -348,6 +375,7 @@ exportMethods(getMixtureWeights)
 exportMethods(getN)
 exportMethods(getNRef)
 exportMethods(getNSamples)
+exportMethods(getP)
 exportMethods(getPath)
 exportMethods(getPgenPtr)
 exportMethods(getPhenotypeCovariates)
@@ -360,9 +388,11 @@ exportMethods(getRefPanel)
 exportMethods(getRegion)
 exportMethods(getResidualizedGenotypes)
 exportMethods(getResidualizedPhenotypes)
+exportMethods(getSE)
 exportMethods(getSampleIds)
 exportMethods(getScaleResiduals)
 exportMethods(getScoreStats)
+exportMethods(getSignificantQtls)
 exportMethods(getSnpIdx)
 exportMethods(getSnpInfo)
 exportMethods(getSnpRanges)
@@ -375,6 +405,7 @@ exportMethods(getSusieFit)
 exportMethods(getTauBlocks)
 exportMethods(getTopLoci)
 exportMethods(getTraitNames)
+exportMethods(getTraitPosition)
 exportMethods(getTraitRun)
 exportMethods(getTraitRuns)
 exportMethods(getTraits)
@@ -386,6 +417,8 @@ exportMethods(getWeights)
 exportMethods(getZ)
 exportMethods(hasGenotypes)
 exportMethods(nSnps)
+exportMethods(overlapTopLoci)
+exportMethods(qtlAssociationPostprocess)
 exportMethods(readAnnotations)
 exportMethods(readGenotypes)
 exportMethods(resolveWeights)
@@ -432,6 +465,7 @@ importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,if_else)
 importFrom(dplyr,inner_join)
+importFrom(dplyr,matches)
 importFrom(dplyr,mutate)
 importFrom(dplyr,pull)
 importFrom(dplyr,rename)
@@ -441,6 +475,7 @@ importFrom(dplyr,slice)
 importFrom(dplyr,summarise)
 importFrom(magrittr,"%>%")
 importFrom(matrixStats,colSds)
+importFrom(metafor,rma)
 importFrom(methods,as)
 importFrom(methods,is)
 importFrom(methods,new)