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
PSCBSoutput2DNAcopy Source code
PureCN-defunct Man page
PureCN-deprecated Man page
add.chr.name Source code
addADField Source code
addAverageCoverage 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
adjustEmpBayes Source code
annotateIntervalsGC Source code
annotateIntervalsMappability Source code
annotateIntervalsOfftarget Source code
annotateIntervalsReptiming Source code
annotateMappingBias Source code
annotatePosteriorsVcf Source code
annotateTargets Man page Source code
annotateVcfTarget Source code
appendComment Source code
bootstrapResults Man page Source code 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
calculateBamCoverageByInterval Man page Source code
calculateGCContentByInterval Man page Source code
calculateIntervalWeights Man page Source code
calculateLogRatio Man page Source code
calculateMappingBias 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
callLOH Man page Source code
callMutationBurden Man page Source code
centromeres Man page
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
checkSeqlevelStyle Source code
checkSymbolsChromosome Source code
checkVcfFieldAvailable Source code
checkVcfNotEmpty Source code
correctCoverageBias Man page Source code
correctCoverageBiasLoess Source code
correctRepTimingBiasLinear Source code
coverageHasCounts Source code
createCoverageGgplot Source code
createCurationFile Man page Source code
createFakeLogRatios Source code
createNormalDatabase Man page Source code
createTargetWeights Man page 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
filterIntervals Man page 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
filterTargets Man page Source code
filterVcfBasic Man page Source code
filterVcfByBQ Source code
filterVcfMuTect Man page Source code
filterVcfMuTect2 Man page Source code
findBestNormal Man page Source code
findCNNLOH Source code
findFocal Man page 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
getCNAobject Source code
getCentromerePositions Source code
getCentromeres Source code
getChrHash Source code
getColScore Source code
getFormat Source code
getFractionLoh Source code
getGeneCalls Source code
getGoF Source code
getNormalIdInVcf Source code
getPruneH Source code
getSDundo Source code
getSegSizes Source code
getSex Source code
getSexChr Source code
getSexFromCoverage Man page Source code
getSexFromRds Source code
getSexFromVcf Man page Source code
getSizeDomState Source code
getTumorIdInVcf Source code
getVariantPosteriors Source code
legend.col Source code
loadSegFile Source code
logFooter Source code
logHeader Source code
matrixTotalPloidyToTumorPloidy Source code
optimizeGrid Source code
padGranges Source code
plotAbs Man page 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
poolCoverage Man page Source code
postprocessLogRatios Source code
predictSomatic Man page Source code
preprocessIntervals Man page Source code
pruneByHclust Source code
pruneByVCF Source code
purecn.DNAcopy.bdry Man page
purecn.example.output Man page
rankResults Source code
readAndCheckVcf Source code
readCoverageCnn Source code
readCoverageFile Man page Source code
readCoverageGatk3 Source code
readCoverageGatk4 Source code
readCurationFile Man page Source code
readNormalPanelVcfLarge Source code
readNormals Source code
remove0MappabilityRegions Source code
removeChr Source code
removeOutliers Source code
runAbsoluteCN Man page Source code
sFakeLogRatio Source code
sRareKaryotype Source code
sampleError Source code
sampleOffset Source code
sampleOffsetFast Source code
segmentationCBS Man page Source code
segmentationPSCBS Man page Source code
setMappingBiasVcf Man page Source code
setPriorVcf Man page 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 documentation built on Nov. 11, 2018, 6 p.m.