API for kauralasoo/seqUtils

Global functions
GRangesListToDataFrame Source code
PWMSimilarityMatrix Source code
addAssociationPosterior Man page Source code
addExpectedPvalue Man page Source code
addMafFromVariantInfo Source code
addOverlappingPeaks Man page Source code
addR2FromLead Man page Source code
addVariantCoords Source code
annotateCredibleSet Man page Source code
asPWMatrixList Source code
aseDataAddGenotypes Man page Source code
betaCorrectSign Source code
betaCorrectSignPairs Source code
binGenesByResidual Source code
calculateBetaDiffMatrix Source code
calculateCQN Man page Source code
calculateClusterMeans Source code
calculateClusterSizes Source code
calculateEnrichment Man page Source code
calculateMean Source code
calculateMeanProportions Source code
calculateNormFactors Source code
calculatePairR2 Source code
calculatePairwiseConcordance Source code
calculatePairwisePi1 Man page Source code
calculatePeakDistance Man page Source code
calculatePermutationPvalues Man page Source code
calculatePi1 Man page Source code
calculateR2FromLead Source code
calculateTPM Man page Source code
calculateTranscriptRatios Source code
censorLog2OR Man page Source code
cisBPImportMotif Source code
cisBPImportRecords Source code
cisBPMotifToPFMatrix Source code
clusterAmbiguousMasters Source code
clusterBetasKmeans Source code
colocGeneAgainstPeaks Source code
colocMolecularQTLs Man page Source code
colocMolecularQTLsByRow Man page Source code
colocQtlGWAS Man page Source code
conditionPalette Man page Source code
constructClustersFromGenePairs Source code
constructCredibleSet Man page Source code
constructExonRanges Source code
constructFastQTLGenePos Man page Source code
constructGWASRanges Source code
constructGeneData Man page Source code
constructGenotypeText Man page Source code
constructIdBatches Source code
constructIntronExonDf Source code
constructMatrixEQTLCovariates Man page Source code
constructMatrixEQTLGenePos Man page Source code
constructQTLtoolsGenePos Man page Source code
constructQtlListForColoc Source code
constructQtlPlotDataFrame Source code
constructVariantRanges Man page Source code
countConditionSpecificOverlaps Source code
credibleSetJaccard Source code
credibleSetPeakOverlaps Man page Source code
credibleSetsToDf Source code
credibleSetsToGranges Source code
dataFrameToGRanges Man page Source code
eigenMTExportGeneMetadata Source code
eigenMTExportGenotypes Man page Source code
eigenMTExportGenotypesByChr Man page Source code
eigenMTImportResults Man page Source code
estimateLeadVariantConcordance Source code
estimateVarianceExplained Man page Source code
exportDataForRasqual Man page Source code
extractAndProcessBetas Source code
extractBetasForQTLPairs Source code
extractBetasFromList Source code
extractChrFromReducedDf Source code
extractConditionFromExpressionList Man page Source code
extractExonsStartEnd Source code
extractGeneData Source code
extractGenesFromExpressionList Man page Source code
extractPvaluesFromList Source code
extractQTLsFromList Man page Source code
extractSubset Source code
extractTrQtlDataFromSE Source code
fastQTLCorrectEigenMT Source code
fastqtlMetadataToCovariates Source code
fastqtlTabixFetchGenes Man page Source code
fastqtlTabixFetchGenesQuick Source code
fastqtlTabixFetchSNPs Man page Source code
fetchGeneASEData Source code
filterASEforPlotting Source code
filterDESeqResults Source code
filterGeneR2 Source code
filterHitsR2 Man page Source code
filterInteractionResults Man page Source code
filterOverlaps Man page Source code
fimoFisherTest Source code
fimoRelativeEnrichment Man page Source code
findAllAssociatedPeaksPerSNP Source code
findCredibleSetOverlaps Source code
findGWASOverlaps Man page Source code
findMinimalSnpPvalues Man page Source code
findMostAssociatedPeakPerSNP Source code
finemapConstructMeta Source code
friendlyNames Source code
gdsToMatrix Man page Source code
getFDR Man page Source code
idVectorToList Source code
identifyAmbiguousMasters Man page Source code
identifyColocHits Source code
identifyLinkedLeadSNPs Source code
identifyUniqueMasters Source code
importAndFilterColocHits Source code
importColocs Source code
importCredibleSets Man page Source code
importFastQTLTable Man page Source code
importGWASSummary Man page Source code
importGwasCatalog Man page Source code
importGwasPvalue Source code
importMotifDisruptions Source code
importPEERFactors Source code
importQTLtoolsTable Man page Source code
importRasqualTable Man page Source code
importSummariesForPlotting Source code
importVariantInformation Man page Source code
leafcutterConstructMeta Source code
leafcutterMetaToGrangesList Source code
listUnion Source code
loadBroadPeaks Man page Source code
loadChrCounts Source code
loadCounts Man page Source code
loadExonCounts Source code
loadFeaturCountsSummary Source code
loadFragmentLengths Man page Source code
loadIntronEventCounts Source code
loadMarkDuplicates Source code
loadNarrowPeaks Man page Source code
loadSalmonCounts Source code
loadVerifyBamID Source code
makeColocPlot Source code
makeMultiplePlots Man page Source code
makeQTLCoveragePlot Source code
makeUnionPeaks Man page Source code
matrixEQTLExtractCisQTLs Source code
matrixExtractPairs Source code
matrixeqtlTestInteraction Man page Source code
maximumFactorPerGene Source code
mbvFindBestMatch Source code
meanVarianceWithinBins Source code
mergeATACandRNAEffects Source code
modifyDNAString Source code
pToZ Man page Source code
performPCA Source code
plotBinnedVariance Source code
plotColoc Source code
plotEQTL Man page Source code
plotGene Source code
plotQTLCompact Source code
plotQtlCol Source code
plotQtlRow Source code
postProcessInteractionPvalues Source code
prefilterColocCandidates Man page Source code
prepareBetasDf Source code
prepareFastqtlMatrix Man page Source code
prepareQTLtoolsMatrix Man page Source code
qtltoolsTabixFetchPhenotypes Man page Source code
quantifyMotifDisruption Man page Source code
quantifyMultipleMotifs Man page Source code
quantifyMultipleVariants Man page Source code
quantileNormaliseCols Source code
quantileNormaliseMatrix Source code
quantileNormaliseRows Source code
quantileNormaliseVector Man page Source code
rangesQueryMeta Source code
rankAtacSummaries Man page Source code
rankTraitsByOverlapSize Source code
rasqualSummariesToGarfieldByChr Source code
reduceDataFrameGRanges Source code
removeLowlyExpressedTranscripts Source code
renameMatrixColumnsInExpressionList Source code
replaceNAsWithRowMeans Source code
runMatrixEQTL Man page Source code
salmonSummarizedExperiment Source code
saveFastqtlMatrices Man page Source code
saveFinemapMatrices Source code
saveMotifListLogos Source code
savePEERData Man page Source code
savePlotList Source code
savePlots Man page Source code
saveQTLToolsMatrices Man page Source code
scanTabixDataFrame Man page Source code
splitIntoBatches Man page Source code
subsampleFisherTest Man page Source code
subsetDNAStringSet Source code
summariseCredibleSets Source code
summaryReplaceCoordinates Source code
summaryReplaceSnpId Source code
tabixFetchASE Source code
tabixFetchGWASSummary Man page Source code
tbl_df2 Man page Source code
testColoc Man page Source code
testInteraction Man page Source code
testInteractionByChromosome Source code
testInteractionLme4 Man page Source code
testInterctionsBetweenPairs Source code
testMultipleInteractions Source code
testThreewayInteraction Man page Source code
tibbleToNamedMatrix Man page Source code
tidyASECounts Source code
tidyDESeq Source code
tidyGenotypeMatrix Man page Source code
tidyTopTable Source code
tidyVector Man page Source code
varianceExplained Man page Source code
wiggleplotrConstructMetadata Man page Source code
wiggleplotrExtractPeaks Source code
wiggleplotrGenotypeColourGroup Source code
wiggpleplotrConstructPeakAnnotations Source code
zScoreNormalize Source code
zToLD Man page Source code
kauralasoo/seqUtils documentation built on Sept. 24, 2018, 1:11 a.m.