API for PureCN
Copy number calling and SNV classification using targeted short read sequencing

Global functions
.CNV.analyze2 Source code
.MoM Source code
.PSCBSgetKnownSegments Source code
.PSCBSinput Source code
.PSCBSoutput2DNAcopy Source code
.add.chr.name Source code
.addADField Source code
.addAverageCoverage Source code
.addAverageWeights Source code
.addCosmicCNT Source code
.addDbField Source code
.addDpField Source code
.addFaField Source code
.addGCData Source code
.addScoreToGr Source code
.addSomaticField Source code
.addSymbols Source code
.add_allelic_imbalance Source code
.add_weights_to_normaldb Source code
.adjustEmpBayes Source code
.annotateIntervalsGC Source code
.annotateIntervalsMappability Source code
.annotateIntervalsOfftarget Source code
.annotateIntervalsReptiming Source code
.annotateMappingBias Source code
.annotatePosteriorsVcf Source code
.annotateVcfTarget Source code
.appendComment Source code
.bootstrapResults Source code
.calcComplexityCopyNumber Source code
.calcExpectedRatio Source code
.calcFractionBalanced Source code
.calcGCmetric Source code
.calcIdealPeaks Source code
.calcLlikSegment Source code
.calcLlikSegmentClonal Source code
.calcLlikSegmentExonLrs Source code
.calcLlikSegmentSubClonal Source code
.calcMsSegment Source code
.calcMsSegmentC Source code
.calcPuritySomaticVariants Source code
.calcSNVLLik Source code
.calcTargetedGenome Source code
.calculateIntervalWeights Source code
.calculateMappingBias Source code
.calculate_allelic_imbalance Source code
.calculate_ccf Source code
.calculate_tumor_normal_noise_ratio Source code
.calibrate_log_ratio Source code
.calibrate_log_ratio_on_off Source code
.checkADField Source code
.checkArgs Source code
.checkColScore Source code
.checkFraction Source code
.checkGCBias Source code
.checkIntervals Source code
.checkLowCoverage Source code
.checkNormalDB Source code
.checkParameters Source code
.checkSeg Source code
.checkSeqlengths Source code
.checkSeqlevelStyle Source code
.checkSymbolsChromosome Source code
.checkTargetWidth Source code
.checkVcfFieldAvailable Source code
.checkVcfNotEmpty Source code
.convertSegGATK4 Source code
.correctCoverageBiasLoess Source code
.correctRepTimingBiasLinear Source code
.coverageHasCounts Source code
.createCoverageGgplot Source code
.createFakeLogRatios Source code
.debugSegmentation Source code
.denoiseSample Source code
.detectCaller Source code
.dropShortUntargetedSeqLevels Source code
.estimateContamination Source code
.excludeIntervals Source code
.extractCountMatrix Source code
.extractMLSNVState Source code
.failedNonAberrant Source code
.filterDuplicatedCandidates Source code
.filterDuplicatedResults Source code
.filterDuplicates Source code
.filterIntervalsChrHash Source code
.filterIntervalsCoverage Source code
.filterIntervalsCreateNormalDB Source code
.filterIntervalsLowHighGC Source code
.filterIntervalsNormalDB Source code
.filterIntervalsNotNA Source code
.filterIntervalsTargetedBase Source code
.filterIntervalsTotalNormalCoverage Source code
.filterVcfByBQ Source code
.findCNNLOH Source code
.findClosestSolution Source code
.findLocalMinima Source code
.fixAllosomeCoverage Source code
.fixAllosomeSegmentation Source code
.fixStartEndPos Source code
.flagBootstrap Source code
.flagResult Source code
.flagResults Source code
.gcGeneToCoverage Source code
.get2DPurityGrid Source code
.getAFPlotGroups Source code
.getArmLocations Source code
.getAverageWeightPV Source code
.getCNAobject Source code
.getCentromerePositions Source code
.getCentromeres Source code
.getChrHash Source code
.getColScore Source code
.getExonLrs Source code
.getFormat Source code
.getFractionLoh Source code
.getGeneCalls Source code
.getGoF Source code
.getLogRatioFormat Source code
.getNormalIdInVcf Source code
.getPruneH Source code
.getSDundo Source code
.getSegFormat Source code
.getSegSizes Source code
.getSex Source code
.getSexChr Source code
.getSexFromRds Source code
.getSizeDomState Source code
.getTumorIdInVcf Source code
.getVariantPosteriors Source code
.isFakeLogRatio Source code
.isRareKaryotype Source code
.legend.col Source code
.logFooter Source code
.logHeader Source code
.matrixTotalPloidyToTumorPloidy Source code
.optimizeGrid Source code
.padGranges Source code
.plotGcBias Source code
.plotIntervalWeights Source code
.plotLogRatios Source code
.plotRepBias Source code
.plotTypeAF Source code
.plotTypeBAF Source code
.plotTypeHist Source code
.plotTypeOverview Source code
.postprocessLogRatios Source code
.pruneByHclust Source code
.pruneByVCF Source code
.rankResults Source code
.readAndCheckVcf Source code
.readCoverageCnn Source code
.readCoverageGatk3 Source code
.readCoverageGatk4 Source code
.readLogRatioFileGATK3 Source code
.readLogRatioFileGATK4 Source code
.readNormalPanelVcfLarge Source code
.readNormals Source code
.remove0MappabilityRegions Source code
.removeChr Source code
.removeOutliers Source code
.sampleError Source code
.sampleOffset Source code
.sampleOffsetFast Source code
.splitIntervals Source code
.standardizeNormals Source code
.stopRuntimeError Source code
.stopUserError Source code
.strip.chr.name Source code
.testGermline Source code
.tileReptiming Source code
.toLines Source code
.updateNumMark Source code
.warnLowCoverageTargets Source code
.writeCoverage Source code
.writeIntervals Source code
.writeQCFile Source code
PureCN-defunct Man page
PureCN-deprecated Man page
annotateTargets Man page Source code
bootstrapResults Man page Source code
calculateBamCoverageByInterval Man page Source code
calculateGCContentByInterval Man page Source code
calculateIntervalWeights Man page Source code
calculateLogRatio Man page Source code
calculateMappingBiasVcf Man page Source code
calculatePowerDetectSomatic Man page Source code
calculateTangentNormal Man page Source code
callAlterations Man page Source code
callAlterationsFromSegmentation Man page Source code
callAmplificationsInLowPurity Man page Source code
callCIN Man page Source code
callLOH Man page Source code
callMutationBurden Man page Source code
centromeres Man page
correctCoverageBias Man page Source code
createCurationFile Man page Source code
createNormalDatabase Man page Source code
createTargetWeights Man page Source code
filterIntervals Man page Source code
filterTargets Man page Source code
filterVcfBasic Man page Source code
filterVcfMuTect Man page Source code
filterVcfMuTect2 Man page Source code
findFocal Man page Source code
getSexFromCoverage Man page Source code
getSexFromVcf Man page Source code
plotAbs Man page Source code
poolCoverage Man page Source code
predictSomatic Man page Source code
preprocessIntervals Man page Source code
processMultipleSamples Man page Source code
purecn.DNAcopy.bdry Man page
purecn.example.output Man page
readCoverageFile Man page Source code
readCurationFile Man page Source code
readLogRatioFile Man page Source code
readSegmentationFile Man page Source code
runAbsoluteCN Man page Source code
segmentationCBS Man page Source code
segmentationHclust Man page Source code
segmentationPSCBS Man page Source code
setMappingBiasVcf Man page Source code
setPriorVcf Man page Source code
PureCN documentation built on Oct. 31, 2019, 2:13 a.m.