extractWIG extractWIG.AbstractCBS extractWIG.CBS extractWIG.PSCBS
all.equal.AbstractCBS all.equal.CBS append append.default
 applyByRegion applyByRegion.PairedPSCBS arrowsC1C2
 arrowsC1C2.PairedPSCBS arrowsDeltaC1C2 arrowsDeltaC1C2.PairedPSCBS
 as.CBS as.DNAcopy as.character.CBS as.data.frame.PSCBS bootstrapCIs
 bootstrapCIs.PairedPSCBS bootstrapDHByRegion
 bootstrapDHByRegion.PairedPSCBS bootstrapTCNandDHByRegion
 callAB callABandHighAI
 callABandHighAI.PairedPSCBS callABandLowC1 callABandLowC1.PairedPSCBS
 callAllelicBalance callAllelicBalance.default callAllelicBalanceByDH
 callAmplifications callArms callArms.CBS
 callExtremeAllelicImbalanceByDH
 callExtremeAllelicImbalanceByDH.PairedPSCBS callGainsAndLosses
 callLOH callLowC1ByC1 callLowC1ByC1.PairedPSCBS callOutliers
 drawCentromeres drawCentromeres.CBS drawChromosomes
 drawChromosomes.CBS drawConfidenceBands
 drawConfidenceBands.PairedPSCBS drawLevels drawLevels.CBS
 drawLevels.DNAcopy drawLevels.PairedPSCBS
 dropChangePoint dropRegion dropRegions
 estimateDeltaAB
 estimateDeltaABBySmallDH estimateDeltaLOH
 estimateDeltaLOHByMinC1ForNonAB estimateHighDHQuantileAtAB
 estimateHighDHQuantileAtAB.PairedPSCBS estimateKappa
 estimateKappaByC1Density estimateMeanForDH
 estimateMeanForDH.PairedPSCBS estimateStandardDeviation
 estimateStandardDeviation.DNAcopy estimateStdDevForHeterozygousBAF
 estimateStdDevForHeterozygousBAF.PairedPSCBS
 extractC1C2 extractCallsByLocus
 extractCallsByLocus.PairedPSCBS
 extractCallsByLocus.CBS extractChromosome
 extractChromosome.AbstractCBS extractChromosomes
 extractChromosomes.AbstractCBS extractChromosomes.CBS
 extractChromosomes.PSCBS extractDeltaC1C2
 extractDeltaC1C2.PairedPSCBS extractLocusLevelC1C2
 extractLocusLevelC1C2.PairedPSCBS extractLocusLevelTCN
 extractLocusLevelTCN.PairedPSCBS extractMinorMajorCNs extractRegion
 extractRegion.AbstractCBS extractRegions extractRegions.AbstractCBS
 extractSegmentMeansByLocus
 extractSegmentMeansByLocus.DNAcopy extractTCNAndDHs getCallStatistics
 getCallStatisticsByArms getCallStatisticsByArms.CBS
 getChromosomeOffsets getChromosomeRanges
 getChromosomeRanges.CBS getChromosomes getChromosomes.DNAcopy getFGA
 getFGG getFGL getFractionOfGenomeAltered getFractionOfGenomeGained
 getFractionOfGenomeLost getLocusData getLocusData.CBS
 getLocusData.PSCBS getSampleName getSampleNames
 getSampleNames.DNAcopy getSegments getSegments.CBS getSignalType
 getSignalType.CBS highlightArmCalls highlightArmCalls.CBS
 highlightCalls highlightCalls.CBS highlightLocusCalls
 highlightLocusCalls.CBS isWholeChromosomeGained
 isWholeChromosomeGained.CBS isWholeChromosomeLost
 isWholeChromosomeLost.CBS joinSegments linesC1C2
 linesC1C2.PairedPSCBS linesDeltaC1C2 linesDeltaC1C2.PairedPSCBS
 mergeNonCalledSegments mergeTwoSegments mergeTwoSegments.CBS
 nbrOfAmplifications nbrOfAmplifications.CBS nbrOfChangePoints
 nbrOfChromosomes nbrOfGains nbrOfGains.CBS nbrOfLoci
 nbrOfLoci.DNAcopy nbrOfLosses nbrOfLosses.CBS nbrOfSamples
 nbrOfSamples.DNAcopy nbrOfSegments nbrOfSegments.DNAcopy plot.CBS
 plot.PairedPSCBS plotC1C2 plotC1C2.PairedPSCBS plotDeltaC1C2
 plotDeltaC1C2.PairedPSCBS
 plotTracksManyChromosomes.CBS
 pointsC1C2
 pointsC1C2.PairedPSCBS pointsDeltaC1C2 pointsDeltaC1C2.PairedPSCBS
 postsegmentTCN postsegmentTCN.PairedPSCBS print.AbstractCBS
 sampleName sampleName<- setLocusData
 setSampleName setSegments signalType
 signalType.CBS signalType<- signalType<-.CBS subset.CBS
 tileChromosomes tileChromosomes.AbstractCBS tileChromosomes.CBS
 tileChromosomes.PairedPSCBS
 writeLocusData writeLocusData.CBS
 writeSegments
extractSegments.AbstractCBS extractSegment.AbstractCBS
 extractSegment extractSegments extractSegments.CBS
 extractSegments.PairedPSCBS
isSegmentSplitter isSegmentSplitter.CBS isSegmentSplitter.PSCBS
 extractCNs extractCNs.AbstractCBS extractCNs.CBS
 extractCNs.PairedPSCBS extractTotalCNs extractTotalCNs.CBS
 getSegmentSizes getSegmentSizes.AbstractCBS getSegmentSizes.CBS
 getSegmentSizes.PSCBS
sampleCNs sampleCNs.AbstractCBS
mergeThreeSegments
callROH callROHOneSegment callROHOneSegment.PairedPSCBS
testROH
pruneBySdUndo updateBoundaries updateBoundaries.CBS
resegment resegment.AbstractCBS resegment.CBS resegment.PairedPSCBS
 hclustCNs pruneByHClust updateMeansTogether updateMeans
drawChangePoints drawChangePoints.AbstractCBS
drawKnownSegments drawKnownSegments.AbstractCBS
drawChangePoints.CBS drawChangePoints.PSCBS
 drawChangePointsC1C2 drawChangePointsC1C2.PairedPSCBS
extractDhSegment extractDhSegment.PairedPSCBS
callNTCN callCopyNeutral callCopyNeutralByTCNofAB
dropChangePoints
calcStatsForCopyNeutralABs calcStatsForCopyNeutralABs.PairedPSCBS
callGainNeutralLoss
callGNL
renameChromosomes renameChromosomes.AbstractCBS
report
writeSegments.DNAcopy
shiftTCN shiftTCN.AbstractCBS shiftTCN.CBS
shiftTCN.PairedPSCBS
getChromosomeOffsets.AbstractCBS getChromosomeRanges.PairedPSCBS
getChromosomeRanges.AbstractCBS
seqOfSegmentsByDP seqOfSegmentsByDP.AbstractCBS
seqOfSegmentsByDP.CBS seqOfSegmentsByDP.PairedPSCBS
seqOfSegmentsByDP.matrix
getChromosomeOffsets.PairedPSCBS getLocusSignalNames
getLocusSignalNames.AbstractCBS getLocusSignalNames.CBS
getLocusSignalNames.PSCBS getSegmentTrackPrefixes
getSegmentTrackPrefixes.AbstractCBS getSegmentTrackPrefixes.CBS
getSegmentTrackPrefixes.PSCBS
pruneByDP
getMeanEstimators getMeanEstimators.AbstractCBS
resegment.NonPairedPSCBS setMeanEstimators
setMeanEstimators.AbstractCBS
resetSegments
getLocusData.NonPairedPSCBS getLocusData.PairedPSCBS
plotTracks plotTracks1 plotTracks2 plotTracksManyChromosomes
getSmoothLocusData
bootstrapSegmentsAndChangepoints
bootstrapSegmentsAndChangepoints.PairedPSCBS
getChangePoints getChangePoints.AbstractCBS
getChangePoints.CBS getChangePoints.PSCBS
clearBootstrapSummaries clearBootstrapSummaries.PairedPSCBS
findBootstrapSummaries findBootstrapSummaries.PairedPSCBS
hasBootstrapSummaries hasBootstrapSummaries.PairedPSCBS
clearCalls clearCalls.AbstractCBS 
extractSegmentDataByLocus extractSegmentDataByLocus.PairedPSCBS
updateMeansC1C2 updateMeansC1C2.PairedPSCBS
encodeCalls encodeCalls.data.frame
callGLAO callGLAO.CBS
unTumorBoost unTumorBoost.PairedPSCBS
isLocallyPhased
isLocallyPhased.PSCBS
