API for kauralasoo/seqUtils
| Global functions | |
|---|---|
| GRangesListToDataFrame | 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 |
| 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 |
| constructMatrixEQTLCovariates | Man page Source code |
| constructMatrixEQTLGenePos | Man page Source code |
| constructQTLtoolsGenePos | Man page 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 |
| 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 |
| fimoRelativeEnrichment | Man page |
| 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 |
| pToZ | Man page Source code |
| performPCA | Source code |
| plotBinnedVariance | 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 |
| quantifyMultipleMotifs | Man page |
| quantifyMultipleVariants | Man page |
| 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 |
| renameMatrixColumnsInExpressionList | Source code |
| replaceNAsWithRowMeans | Source code |
| runMatrixEQTL | Man page Source code |
| salmonSummarizedExperiment | Source code |
| saveFastqtlMatrices | Man page Source code |
| saveFinemapMatrices | 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 |
| 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 |
