PSCBS-package	PSCBS-package
AbstractCBS	AbstractCBS
AbstractCBS$load	load.AbstractCBS
AbstractCBS.adjustPloidyScale	ploidy.AbstractCBS
AbstractCBS.append	append.AbstractCBS
AbstractCBS.as.data.frame	as.data.frame.AbstractCBS
AbstractCBS.dropChangePoint	mergeTwoSegments.AbstractCBS
AbstractCBS.dropChangePoints	dropChangePoints.AbstractCBS
AbstractCBS.dropRegion	dropRegions.AbstractCBS
AbstractCBS.dropRegions	dropRegions.AbstractCBS
AbstractCBS.getChromosomes	getChromosomes.AbstractCBS
AbstractCBS.getLocusData	getLocusData.AbstractCBS
AbstractCBS.getSampleName	getSampleName.AbstractCBS
AbstractCBS.getSegments	getSegments.AbstractCBS
AbstractCBS.hclustCNs	hclustCNs.AbstractCBS
AbstractCBS.load	load.AbstractCBS
AbstractCBS.mergeThreeSegments	mergeThreeSegments.AbstractCBS
AbstractCBS.mergeTwoSegments	mergeTwoSegments.AbstractCBS
AbstractCBS.nbrOfChangePoints	nbrOfChangePoints.AbstractCBS
AbstractCBS.nbrOfChromosomes	nbrOfChromosomes.AbstractCBS
AbstractCBS.nbrOfLoci	nbrOfLoci.AbstractCBS
AbstractCBS.nbrOfSegments	nbrOfSegments.AbstractCBS
AbstractCBS.normalizeTotalCNs	normalizeTotalCNs.AbstractCBS
AbstractCBS.ploidy	ploidy.AbstractCBS
AbstractCBS.ploidy<-	ploidy.AbstractCBS
AbstractCBS.plotTracks	plotTracks.AbstractCBS
AbstractCBS.pruneByDP	pruneByDP.AbstractCBS
AbstractCBS.pruneByHClust	pruneByHClust.AbstractCBS
AbstractCBS.report	report.AbstractCBS
AbstractCBS.resetSegments	resetSegments.AbstractCBS
AbstractCBS.sampleName	getSampleName.AbstractCBS
AbstractCBS.sampleName<-	setSampleName.AbstractCBS
AbstractCBS.save	save.AbstractCBS
AbstractCBS.setLocusData	getLocusData.AbstractCBS
AbstractCBS.setPloidy	ploidy.AbstractCBS
AbstractCBS.setSampleName	setSampleName.AbstractCBS
AbstractCBS.setSegments	getSegments.AbstractCBS
AbstractCBS.updateMeans	updateMeans.AbstractCBS
AbstractCBS.updateMeansTogether	updateMeansTogether.AbstractCBS
adjustPloidyScale	ploidy.AbstractCBS
adjustPloidyScale,AbstractCBS-method	ploidy.AbstractCBS
adjustPloidyScale.AbstractCBS	ploidy.AbstractCBS
adjustPloidyScale.PairedPSCBS	ploidy.AbstractCBS
all.equal.AbstractCBS	Non-documented_objects
all.equal.CBS	Non-documented_objects
append	Non-documented_objects
append,AbstractCBS-method	append.AbstractCBS
append,CBS-method	append.CBS
append,PSCBS-method	append.PSCBS
append.AbstractCBS	append.AbstractCBS
append.CBS	append.CBS
append.default	Non-documented_objects
append.PSCBS	append.PSCBS
applyByRegion	Non-documented_objects
applyByRegion.PairedPSCBS	Non-documented_objects
arrowsC1C2	Non-documented_objects
arrowsC1C2.PairedPSCBS	Non-documented_objects
arrowsDeltaC1C2	Non-documented_objects
arrowsDeltaC1C2.PairedPSCBS	Non-documented_objects
as.CBS	Non-documented_objects
as.CBS,DNAcopy-method	as.CBS.DNAcopy
as.CBS.DNAcopy	as.CBS.DNAcopy
as.character.CBS	Non-documented_objects
as.data.frame,AbstractCBS-method	as.data.frame.AbstractCBS
as.data.frame,CBS-method	as.data.frame.CBS
as.data.frame.AbstractCBS	as.data.frame.AbstractCBS
as.data.frame.CBS	as.data.frame.CBS
as.data.frame.PSCBS	Non-documented_objects
as.DNAcopy	Non-documented_objects
as.DNAcopy,CBS-method	as.DNAcopy.CBS
as.DNAcopy.CBS	as.DNAcopy.CBS
bootstrapCIs	Non-documented_objects
bootstrapCIs.PairedPSCBS	Non-documented_objects
bootstrapDHByRegion	Non-documented_objects
bootstrapDHByRegion.PairedPSCBS	Non-documented_objects
bootstrapSegmentsAndChangepoints	Non-documented_objects
bootstrapSegmentsAndChangepoints.PairedPSCBS	Non-documented_objects
bootstrapTCNandDHByRegion	Non-documented_objects
bootstrapTCNandDHByRegion,PairedPSCBS-method	bootstrapTCNandDHByRegion.PairedPSCBS
bootstrapTCNandDHByRegion.PairedPSCBS	bootstrapTCNandDHByRegion.PairedPSCBS
calcStatsForCopyNeutralABs	Non-documented_objects
calcStatsForCopyNeutralABs.PairedPSCBS	Non-documented_objects
callAB	Non-documented_objects
callAB,PairedPSCBS-method	callAB.PairedPSCBS
callAB.PairedPSCBS	callAB.PairedPSCBS
callABandHighAI	Non-documented_objects
callABandHighAI.PairedPSCBS	Non-documented_objects
callABandLowC1	Non-documented_objects
callABandLowC1.PairedPSCBS	Non-documented_objects
callAllelicBalance	Non-documented_objects
callAllelicBalance,PairedPSCBS-method	callAB.PairedPSCBS
callAllelicBalance.default	Non-documented_objects
callAllelicBalance.PairedPSCBS	callAB.PairedPSCBS
callAllelicBalanceByDH	Non-documented_objects
callAllelicBalanceByDH,PairedPSCBS-method	callAllelicBalanceByDH.PairedPSCBS
callAllelicBalanceByDH.PairedPSCBS	callAllelicBalanceByDH.PairedPSCBS
callAmplifications	Non-documented_objects
callAmplifications,CBS-method	callAmplifications.CBS
callAmplifications.CBS	callAmplifications.CBS
callArms	Non-documented_objects
callArms.CBS	Non-documented_objects
callCopyNeutral	Non-documented_objects
callCopyNeutral,PairedPSCBS-method	callCopyNeutral.PairedPSCBS
callCopyNeutral.PairedPSCBS	callCopyNeutral.PairedPSCBS
callCopyNeutralByTCNofAB	Non-documented_objects
callCopyNeutralByTCNofAB,PairedPSCBS-method	callCopyNeutralByTCNofAB.PairedPSCBS
callCopyNeutralByTCNofAB.PairedPSCBS	callCopyNeutralByTCNofAB.PairedPSCBS
callExtremeAllelicImbalanceByDH	Non-documented_objects
callExtremeAllelicImbalanceByDH.PairedPSCBS	Non-documented_objects
callGainNeutralLoss	Non-documented_objects
callGainNeutralLoss,PairedPSCBS-method	callGNL.PairedPSCBS
callGainNeutralLoss.PairedPSCBS	callGNL.PairedPSCBS
callGainsAndLosses	Non-documented_objects
callGainsAndLosses,CBS-method	callGainsAndLosses.CBS
callGainsAndLosses.CBS	callGainsAndLosses.CBS
callGLAO	Non-documented_objects
callGLAO.CBS	Non-documented_objects
callGNL	Non-documented_objects
callGNL,PairedPSCBS-method	callGNL.PairedPSCBS
callGNL.PairedPSCBS	callGNL.PairedPSCBS
callGNLByTCNofAB	callGNL.PairedPSCBS
callGNLByTCNofAB,PairedPSCBS-method	callGNL.PairedPSCBS
callGNLByTCNofAB.PairedPSCBS	callGNL.PairedPSCBS
callGNLByTCNofABv1	callGNL.PairedPSCBS
callGNLByTCNofABv1,PairedPSCBS-method	callGNL.PairedPSCBS
callGNLByTCNofABv1.PairedPSCBS	callGNL.PairedPSCBS
callLOH	Non-documented_objects
callLOH,PairedPSCBS-method	callLOH.PairedPSCBS
callLOH.PairedPSCBS	callLOH.PairedPSCBS
callLowC1ByC1	Non-documented_objects
callLowC1ByC1.PairedPSCBS	Non-documented_objects
callNTCN	Non-documented_objects
callNTCN,PairedPSCBS-method	callCopyNeutral.PairedPSCBS
callNTCN.PairedPSCBS	callCopyNeutral.PairedPSCBS
callOutliers	Non-documented_objects
callOutliers,CBS-method	callOutliers.CBS
callOutliers.CBS	callOutliers.CBS
callROH	Non-documented_objects
callROH,PairedPSCBS-method	callROH.PairedPSCBS
callROH.NonPairedPSCBS	callROH.PairedPSCBS
callROH.PairedPSCBS	callROH.PairedPSCBS
callROHOneSegment	Non-documented_objects
callROHOneSegment.PairedPSCBS	Non-documented_objects
callSegmentationOutliers	callSegmentationOutliers
callSegmentationOutliers.data.frame	callSegmentationOutliers
callSegmentationOutliers.default	callSegmentationOutliers
CBS	CBS
CBS.append	append.CBS
CBS.as.data.frame	as.data.frame.CBS
CBS.as.DNAcopy	as.DNAcopy.CBS
CBS.callAmplifications	callAmplifications.CBS
CBS.callGainsAndLosses	callGainsAndLosses.CBS
CBS.callOutliers	callOutliers.CBS
CBS.estimateStandardDeviation	estimateStandardDeviation.CBS
CBS.extractSegmentMeansByLocus	extractSegmentMeansByLocus.CBS
CBS.getCallStatistics	getCallStatistics.CBS
CBS.getFGA	getFractionOfGenomeLost.CBS
CBS.getFGG	getFractionOfGenomeLost.CBS
CBS.getFGL	getFractionOfGenomeLost.CBS
CBS.getFractionOfGenomeAltered	getFractionOfGenomeLost.CBS
CBS.getFractionOfGenomeGained	getFractionOfGenomeLost.CBS
CBS.getFractionOfGenomeLost	getFractionOfGenomeLost.CBS
CBS.getSmoothLocusData	getSmoothLocusData.CBS
CBS.joinSegments	joinSegments.CBS
CBS.mergeNonCalledSegments	mergeNonCalledSegments.CBS
CBS.plotTracks	plotTracks.CBS
CBS.pruneBySdUndo	pruneBySdUndo.CBS
CBS.writeSegments	writeSegments.CBS
clearBootstrapSummaries	Non-documented_objects
clearBootstrapSummaries.PairedPSCBS	Non-documented_objects
clearCalls	Non-documented_objects
clearCalls.AbstractCBS	Non-documented_objects
DNAcopy.as.CBS	as.CBS.DNAcopy
drawCentromeres	Non-documented_objects
drawCentromeres.CBS	Non-documented_objects
drawChangePoints	Non-documented_objects
drawChangePoints.AbstractCBS	Non-documented_objects
drawChangePoints.CBS	Non-documented_objects
drawChangePoints.PSCBS	Non-documented_objects
drawChangePointsC1C2	Non-documented_objects
drawChangePointsC1C2.PairedPSCBS	Non-documented_objects
drawChromosomes	Non-documented_objects
drawChromosomes.CBS	Non-documented_objects
drawConfidenceBands	Non-documented_objects
drawConfidenceBands.PairedPSCBS	Non-documented_objects
drawKnownSegments	Non-documented_objects
drawKnownSegments.AbstractCBS	Non-documented_objects
drawLevels	Non-documented_objects
drawLevels.CBS	Non-documented_objects
drawLevels.DNAcopy	Non-documented_objects
drawLevels.PairedPSCBS	Non-documented_objects
dropChangePoint	Non-documented_objects
dropChangePoint,AbstractCBS-method	mergeTwoSegments.AbstractCBS
dropChangePoint.AbstractCBS	mergeTwoSegments.AbstractCBS
dropChangePoints	Non-documented_objects
dropChangePoints,AbstractCBS-method	dropChangePoints.AbstractCBS
dropChangePoints.AbstractCBS	dropChangePoints.AbstractCBS
dropRegion	Non-documented_objects
dropRegion,AbstractCBS-method	dropRegions.AbstractCBS
dropRegion.AbstractCBS	dropRegions.AbstractCBS
dropRegions	Non-documented_objects
dropRegions,AbstractCBS-method	dropRegions.AbstractCBS
dropRegions.AbstractCBS	dropRegions.AbstractCBS
dropSegmentationOutliers	callSegmentationOutliers
dropSegmentationOutliers.data.frame	callSegmentationOutliers
dropSegmentationOutliers.default	callSegmentationOutliers
encodeCalls	Non-documented_objects
encodeCalls.data.frame	Non-documented_objects
estimateDeltaAB	Non-documented_objects
estimateDeltaAB,PairedPSCBS-method	estimateDeltaAB.PairedPSCBS
estimateDeltaAB.PairedPSCBS	estimateDeltaAB.PairedPSCBS
estimateDeltaABBySmallDH	Non-documented_objects
estimateDeltaABBySmallDH,PairedPSCBS-method	estimateDeltaABBySmallDH.PairedPSCBS
estimateDeltaABBySmallDH.PairedPSCBS	estimateDeltaABBySmallDH.PairedPSCBS
estimateDeltaCN	estimateDeltaCN.PairedPSCBS
estimateDeltaCN,PairedPSCBS-method	estimateDeltaCN.PairedPSCBS
estimateDeltaCN.CBS	estimateDeltaCN.PairedPSCBS
estimateDeltaCN.PairedPSCBS	estimateDeltaCN.PairedPSCBS
estimateDeltaLOH	Non-documented_objects
estimateDeltaLOH,PairedPSCBS-method	estimateDeltaLOH.PairedPSCBS
estimateDeltaLOH.PairedPSCBS	estimateDeltaLOH.PairedPSCBS
estimateDeltaLOHByMinC1ForNonAB	Non-documented_objects
estimateDeltaLOHByMinC1ForNonAB,PairedPSCBS-method	estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS
estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS	estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS
estimateHighDHQuantileAtAB	Non-documented_objects
estimateHighDHQuantileAtAB.PairedPSCBS	Non-documented_objects
estimateKappa	Non-documented_objects
estimateKappa,PairedPSCBS-method	estimateKappa.PairedPSCBS
estimateKappa.PairedPSCBS	estimateKappa.PairedPSCBS
estimateKappaByC1Density	Non-documented_objects
estimateKappaByC1Density,PairedPSCBS-method	estimateKappaByC1Density.PairedPSCBS
estimateKappaByC1Density.PairedPSCBS	estimateKappaByC1Density.PairedPSCBS
estimateMeanForDH	Non-documented_objects
estimateMeanForDH.PairedPSCBS	Non-documented_objects
estimateStandardDeviation	Non-documented_objects
estimateStandardDeviation,CBS-method	estimateStandardDeviation.CBS
estimateStandardDeviation.CBS	estimateStandardDeviation.CBS
estimateStandardDeviation.DNAcopy	Non-documented_objects
estimateStdDevForHeterozygousBAF	Non-documented_objects
estimateStdDevForHeterozygousBAF.PairedPSCBS	Non-documented_objects
exampleData	exampleData
exampleData.default	exampleData
extractC1C2	Non-documented_objects
extractC1C2,PairedPSCBS-method	extractMinorMajorCNs.PairedPSCBS
extractC1C2.PairedPSCBS	extractMinorMajorCNs.PairedPSCBS
extractCallsByLocus	Non-documented_objects
extractCallsByLocus.CBS	Non-documented_objects
extractCallsByLocus.PairedPSCBS	Non-documented_objects
extractChromosome	Non-documented_objects
extractChromosome.AbstractCBS	Non-documented_objects
extractChromosomes	Non-documented_objects
extractChromosomes.AbstractCBS	Non-documented_objects
extractChromosomes.CBS	Non-documented_objects
extractChromosomes.PSCBS	Non-documented_objects
extractCNs	Non-documented_objects
extractCNs.AbstractCBS	Non-documented_objects
extractCNs.CBS	Non-documented_objects
extractCNs.PairedPSCBS	Non-documented_objects
extractDeltaC1C2	Non-documented_objects
extractDeltaC1C2.PairedPSCBS	Non-documented_objects
extractDhSegment	Non-documented_objects
extractDhSegment.PairedPSCBS	Non-documented_objects
extractLocusLevelC1C2	Non-documented_objects
extractLocusLevelC1C2.PairedPSCBS	Non-documented_objects
extractLocusLevelTCN	Non-documented_objects
extractLocusLevelTCN.PairedPSCBS	Non-documented_objects
extractMinorMajorCNs	Non-documented_objects
extractMinorMajorCNs,PairedPSCBS-method	extractMinorMajorCNs.PairedPSCBS
extractMinorMajorCNs.PairedPSCBS	extractMinorMajorCNs.PairedPSCBS
extractRegion	Non-documented_objects
extractRegion.AbstractCBS	Non-documented_objects
extractRegions	Non-documented_objects
extractRegions.AbstractCBS	Non-documented_objects
extractSegment	Non-documented_objects
extractSegment.AbstractCBS	Non-documented_objects
extractSegmentDataByLocus	Non-documented_objects
extractSegmentDataByLocus.PairedPSCBS	Non-documented_objects
extractSegmentMeansByLocus	Non-documented_objects
extractSegmentMeansByLocus,CBS-method	extractSegmentMeansByLocus.CBS
extractSegmentMeansByLocus.CBS	extractSegmentMeansByLocus.CBS
extractSegmentMeansByLocus.DNAcopy	Non-documented_objects
extractSegments	Non-documented_objects
extractSegments.AbstractCBS	Non-documented_objects
extractSegments.CBS	Non-documented_objects
extractSegments.PairedPSCBS	Non-documented_objects
extractTCNAndDHs	Non-documented_objects
extractTCNAndDHs,PairedPSCBS-method	extractTCNAndDHs.PairedPSCBS
extractTCNAndDHs.PairedPSCBS	extractTCNAndDHs.PairedPSCBS
extractTotalCNs	Non-documented_objects
extractTotalCNs.CBS	Non-documented_objects
extractWIG	Non-documented_objects
extractWIG.AbstractCBS	Non-documented_objects
extractWIG.CBS	Non-documented_objects
extractWIG.PSCBS	Non-documented_objects
findBootstrapSummaries	Non-documented_objects
findBootstrapSummaries.PairedPSCBS	Non-documented_objects
findLargeGaps	findLargeGaps
findLargeGaps.data.frame	findLargeGaps
findLargeGaps.default	findLargeGaps
findNeutralCopyNumberState	findNeutralCopyNumberState
findNeutralCopyNumberState.default	findNeutralCopyNumberState
gapsToSegments	gapsToSegments.data.frame
gapsToSegments.data.frame	gapsToSegments.data.frame
getBootstrapLocusSets	getBootstrapLocusSets.PairedPSCBS
getBootstrapLocusSets,PairedPSCBS-method	getBootstrapLocusSets.PairedPSCBS
getBootstrapLocusSets.PairedPSCBS	getBootstrapLocusSets.PairedPSCBS
getCallStatistics	Non-documented_objects
getCallStatistics,CBS-method	getCallStatistics.CBS
getCallStatistics.CBS	getCallStatistics.CBS
getCallStatisticsByArms	Non-documented_objects
getCallStatisticsByArms.CBS	Non-documented_objects
getChangePoints	Non-documented_objects
getChangePoints.AbstractCBS	Non-documented_objects
getChangePoints.CBS	Non-documented_objects
getChangePoints.PSCBS	Non-documented_objects
getChromosomeOffsets	Non-documented_objects
getChromosomeOffsets.AbstractCBS	Non-documented_objects
getChromosomeOffsets.PairedPSCBS	Non-documented_objects
getChromosomeRanges	Non-documented_objects
getChromosomeRanges.AbstractCBS	Non-documented_objects
getChromosomeRanges.CBS	Non-documented_objects
getChromosomeRanges.PairedPSCBS	Non-documented_objects
getChromosomes	Non-documented_objects
getChromosomes,AbstractCBS-method	getChromosomes.AbstractCBS
getChromosomes.AbstractCBS	getChromosomes.AbstractCBS
getChromosomes.DNAcopy	Non-documented_objects
getFGA	Non-documented_objects
getFGA,CBS-method	getFractionOfGenomeLost.CBS
getFGA.CBS	getFractionOfGenomeLost.CBS
getFGG	Non-documented_objects
getFGG,CBS-method	getFractionOfGenomeLost.CBS
getFGG.CBS	getFractionOfGenomeLost.CBS
getFGL	Non-documented_objects
getFGL,CBS-method	getFractionOfGenomeLost.CBS
getFGL.CBS	getFractionOfGenomeLost.CBS
getFractionOfGenomeAltered	Non-documented_objects
getFractionOfGenomeAltered,CBS-method	getFractionOfGenomeLost.CBS
getFractionOfGenomeAltered.CBS	getFractionOfGenomeLost.CBS
getFractionOfGenomeGained	Non-documented_objects
getFractionOfGenomeGained,CBS-method	getFractionOfGenomeLost.CBS
getFractionOfGenomeGained.CBS	getFractionOfGenomeLost.CBS
getFractionOfGenomeLost	Non-documented_objects
getFractionOfGenomeLost,CBS-method	getFractionOfGenomeLost.CBS
getFractionOfGenomeLost.CBS	getFractionOfGenomeLost.CBS
getLocusData	Non-documented_objects
getLocusData,AbstractCBS-method	getLocusData.AbstractCBS
getLocusData.AbstractCBS	getLocusData.AbstractCBS
getLocusData.CBS	Non-documented_objects
getLocusData.NonPairedPSCBS	Non-documented_objects
getLocusData.PairedPSCBS	Non-documented_objects
getLocusData.PSCBS	Non-documented_objects
getLocusSignalNames	Non-documented_objects
getLocusSignalNames.AbstractCBS	Non-documented_objects
getLocusSignalNames.CBS	Non-documented_objects
getLocusSignalNames.PSCBS	Non-documented_objects
getMeanEstimators	Non-documented_objects
getMeanEstimators.AbstractCBS	Non-documented_objects
getSampleName	Non-documented_objects
getSampleName,AbstractCBS-method	getSampleName.AbstractCBS
getSampleName.AbstractCBS	getSampleName.AbstractCBS
getSampleNames	Non-documented_objects
getSampleNames.DNAcopy	Non-documented_objects
getSegments	Non-documented_objects
getSegments,AbstractCBS-method	getSegments.AbstractCBS
getSegments,PSCBS-method	getSegments.PSCBS
getSegments.AbstractCBS	getSegments.AbstractCBS
getSegments.CBS	Non-documented_objects
getSegments.PSCBS	getSegments.PSCBS
getSegmentSizes	Non-documented_objects
getSegmentSizes.AbstractCBS	Non-documented_objects
getSegmentSizes.CBS	Non-documented_objects
getSegmentSizes.PSCBS	Non-documented_objects
getSegmentTrackPrefixes	Non-documented_objects
getSegmentTrackPrefixes.AbstractCBS	Non-documented_objects
getSegmentTrackPrefixes.CBS	Non-documented_objects
getSegmentTrackPrefixes.PSCBS	Non-documented_objects
getSignalType	Non-documented_objects
getSignalType.CBS	Non-documented_objects
getSmoothLocusData	Non-documented_objects
getSmoothLocusData,CBS-method	getSmoothLocusData.CBS
getSmoothLocusData.CBS	getSmoothLocusData.CBS
hasBootstrapSummaries	Non-documented_objects
hasBootstrapSummaries.PairedPSCBS	Non-documented_objects
hclustCNs	Non-documented_objects
hclustCNs,AbstractCBS-method	hclustCNs.AbstractCBS
hclustCNs.AbstractCBS	hclustCNs.AbstractCBS
highlightArmCalls	Non-documented_objects
highlightArmCalls.CBS	Non-documented_objects
highlightCalls	Non-documented_objects
highlightCalls.CBS	Non-documented_objects
highlightLocusCalls	Non-documented_objects
highlightLocusCalls.CBS	Non-documented_objects
installDNAcopy	installDNAcopy
installDNAcopy.default	installDNAcopy
isLocallyPhased	Non-documented_objects
isLocallyPhased.PSCBS	Non-documented_objects
isSegmentSplitter	Non-documented_objects
isSegmentSplitter.CBS	Non-documented_objects
isSegmentSplitter.PSCBS	Non-documented_objects
isWholeChromosomeGained	Non-documented_objects
isWholeChromosomeGained.CBS	Non-documented_objects
isWholeChromosomeLost	Non-documented_objects
isWholeChromosomeLost.CBS	Non-documented_objects
joinSegments	Non-documented_objects
joinSegments,CBS-method	joinSegments.CBS
joinSegments.CBS	joinSegments.CBS
linesC1C2	Non-documented_objects
linesC1C2.PairedPSCBS	Non-documented_objects
linesDeltaC1C2	Non-documented_objects
linesDeltaC1C2.PairedPSCBS	Non-documented_objects
load	load.AbstractCBS
load,AbstractCBS-method	load.AbstractCBS
load.AbstractCBS	load.AbstractCBS
mergeNonCalledSegments	Non-documented_objects
mergeNonCalledSegments,CBS-method	mergeNonCalledSegments.CBS
mergeNonCalledSegments.CBS	mergeNonCalledSegments.CBS
mergeThreeSegments	Non-documented_objects
mergeThreeSegments,AbstractCBS-method	mergeThreeSegments.AbstractCBS
mergeThreeSegments.AbstractCBS	mergeThreeSegments.AbstractCBS
mergeTwoSegments	Non-documented_objects
mergeTwoSegments,AbstractCBS-method	mergeTwoSegments.AbstractCBS
mergeTwoSegments,PairedPSCBS-method	mergeTwoSegments.PairedPSCBS
mergeTwoSegments.AbstractCBS	mergeTwoSegments.AbstractCBS
mergeTwoSegments.CBS	Non-documented_objects
mergeTwoSegments.PairedPSCBS	mergeTwoSegments.PairedPSCBS
nbrOfAmplifications	Non-documented_objects
nbrOfAmplifications.CBS	Non-documented_objects
nbrOfChangePoints	Non-documented_objects
nbrOfChangePoints,AbstractCBS-method	nbrOfChangePoints.AbstractCBS
nbrOfChangePoints.AbstractCBS	nbrOfChangePoints.AbstractCBS
nbrOfChromosomes	Non-documented_objects
nbrOfChromosomes,AbstractCBS-method	nbrOfChromosomes.AbstractCBS
nbrOfChromosomes.AbstractCBS	nbrOfChromosomes.AbstractCBS
nbrOfGains	Non-documented_objects
nbrOfGains.CBS	Non-documented_objects
nbrOfLoci	Non-documented_objects
nbrOfLoci,AbstractCBS-method	nbrOfLoci.AbstractCBS
nbrOfLoci.AbstractCBS	nbrOfLoci.AbstractCBS
nbrOfLoci.DNAcopy	Non-documented_objects
nbrOfLosses	Non-documented_objects
nbrOfLosses.CBS	Non-documented_objects
nbrOfSamples	Non-documented_objects
nbrOfSamples.DNAcopy	Non-documented_objects
nbrOfSegments	Non-documented_objects
nbrOfSegments,AbstractCBS-method	nbrOfSegments.AbstractCBS
nbrOfSegments.AbstractCBS	nbrOfSegments.AbstractCBS
nbrOfSegments.DNAcopy	Non-documented_objects
Non-documented objects	Non-documented_objects
NonPairedPSCBS	NonPairedPSCBS
normalizeTotalCNs	normalizeTotalCNs.AbstractCBS
normalizeTotalCNs,AbstractCBS-method	normalizeTotalCNs.AbstractCBS
normalizeTotalCNs.AbstractCBS	normalizeTotalCNs.AbstractCBS
normalizeTotalCNs.PSCBS	normalizeTotalCNs.AbstractCBS
PairedPSCBS	PairedPSCBS
PairedPSCBS.bootstrapTCNandDHByRegion	bootstrapTCNandDHByRegion.PairedPSCBS
PairedPSCBS.callAB	callAB.PairedPSCBS
PairedPSCBS.callAllelicBalance	callAB.PairedPSCBS
PairedPSCBS.callAllelicBalanceByDH	callAllelicBalanceByDH.PairedPSCBS
PairedPSCBS.callCopyNeutral	callCopyNeutral.PairedPSCBS
PairedPSCBS.callCopyNeutralByTCNofAB	callCopyNeutralByTCNofAB.PairedPSCBS
PairedPSCBS.callGainNeutralLoss	callGNL.PairedPSCBS
PairedPSCBS.callGNL	callGNL.PairedPSCBS
PairedPSCBS.callGNLByTCNofAB	callGNL.PairedPSCBS
PairedPSCBS.callGNLByTCNofABv1	callGNL.PairedPSCBS
PairedPSCBS.callLOH	callLOH.PairedPSCBS
PairedPSCBS.callNTCN	callCopyNeutral.PairedPSCBS
PairedPSCBS.callROH	callROH.PairedPSCBS
PairedPSCBS.estimateDeltaAB	estimateDeltaAB.PairedPSCBS
PairedPSCBS.estimateDeltaABBySmallDH	estimateDeltaABBySmallDH.PairedPSCBS
PairedPSCBS.estimateDeltaCN	estimateDeltaCN.PairedPSCBS
PairedPSCBS.estimateDeltaLOH	estimateDeltaLOH.PairedPSCBS
PairedPSCBS.estimateDeltaLOHByMinC1ForNonAB	estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS
PairedPSCBS.estimateKappa	estimateKappa.PairedPSCBS
PairedPSCBS.estimateKappaByC1Density	estimateKappaByC1Density.PairedPSCBS
PairedPSCBS.extractC1C2	extractMinorMajorCNs.PairedPSCBS
PairedPSCBS.extractMinorMajorCNs	extractMinorMajorCNs.PairedPSCBS
PairedPSCBS.extractTCNAndDHs	extractTCNAndDHs.PairedPSCBS
PairedPSCBS.getBootstrapLocusSets	getBootstrapLocusSets.PairedPSCBS
PairedPSCBS.mergeTwoSegments	mergeTwoSegments.PairedPSCBS
PairedPSCBS.plotTracks	plotTracks.PairedPSCBS
PairedPSCBS.plotTracks1	plotTracks.PairedPSCBS
PairedPSCBS.plotTracks2	plotTracks.PairedPSCBS
PairedPSCBS.plotTracksManyChromosomes	plotTracks.PairedPSCBS
ploidy	ploidy.AbstractCBS
ploidy,AbstractCBS-method	ploidy.AbstractCBS
ploidy.AbstractCBS	ploidy.AbstractCBS
ploidy<-	ploidy.AbstractCBS
ploidy<-,AbstractCBS-method	ploidy.AbstractCBS
ploidy<-.AbstractCBS	ploidy.AbstractCBS
plot	plotTracks.PairedPSCBS
plot.CBS	Non-documented_objects
plot.PairedPSCBS	Non-documented_objects
plotC1C2	Non-documented_objects
plotC1C2.PairedPSCBS	Non-documented_objects
plotDeltaC1C2	Non-documented_objects
plotDeltaC1C2.PairedPSCBS	Non-documented_objects
plotTracks	Non-documented_objects
plotTracks,AbstractCBS-method	plotTracks.AbstractCBS
plotTracks,CBS-method	plotTracks.CBS
plotTracks,PairedPSCBS-method	plotTracks.PairedPSCBS
plotTracks.AbstractCBS	plotTracks.AbstractCBS
plotTracks.CBS	plotTracks.CBS
plotTracks.PairedPSCBS	plotTracks.PairedPSCBS
plotTracks1	Non-documented_objects
plotTracks1,PairedPSCBS-method	plotTracks.PairedPSCBS
plotTracks1.PairedPSCBS	plotTracks.PairedPSCBS
plotTracks2	Non-documented_objects
plotTracks2,PairedPSCBS-method	plotTracks.PairedPSCBS
plotTracks2.PairedPSCBS	plotTracks.PairedPSCBS
plotTracksManyChromosomes	Non-documented_objects
plotTracksManyChromosomes,PairedPSCBS-method	plotTracks.PairedPSCBS
plotTracksManyChromosomes.CBS	Non-documented_objects
plotTracksManyChromosomes.PairedPSCBS	plotTracks.PairedPSCBS
pointsC1C2	Non-documented_objects
pointsC1C2.PairedPSCBS	Non-documented_objects
pointsDeltaC1C2	Non-documented_objects
pointsDeltaC1C2.PairedPSCBS	Non-documented_objects
postsegmentTCN	Non-documented_objects
postsegmentTCN.PairedPSCBS	Non-documented_objects
print.AbstractCBS	Non-documented_objects
pruneByDP	Non-documented_objects
pruneByDP,AbstractCBS-method	pruneByDP.AbstractCBS
pruneByDP.AbstractCBS	pruneByDP.AbstractCBS
pruneByHClust	Non-documented_objects
pruneByHClust,AbstractCBS-method	pruneByHClust.AbstractCBS
pruneByHClust.AbstractCBS	pruneByHClust.AbstractCBS
pruneBySdUndo	Non-documented_objects
pruneBySdUndo,CBS-method	pruneBySdUndo.CBS
pruneBySdUndo.CBS	pruneBySdUndo.CBS
PSCBS	PSCBS
PSCBS.append	append.PSCBS
PSCBS.getSegments	getSegments.PSCBS
PSCBS.writeSegments	writeSegments.PSCBS
randomSeed	randomSeed
renameChromosomes	Non-documented_objects
renameChromosomes.AbstractCBS	Non-documented_objects
report	Non-documented_objects
report,AbstractCBS-method	report.AbstractCBS
report.AbstractCBS	report.AbstractCBS
resegment	Non-documented_objects
resegment.AbstractCBS	Non-documented_objects
resegment.CBS	Non-documented_objects
resegment.NonPairedPSCBS	Non-documented_objects
resegment.PairedPSCBS	Non-documented_objects
resetSegments	Non-documented_objects
resetSegments,AbstractCBS-method	resetSegments.AbstractCBS
resetSegments.AbstractCBS	resetSegments.AbstractCBS
RestructPSCBS	Restructuring_AbstractCBS_objects
Restructuring AbstractCBS objects	Restructuring_AbstractCBS_objects
sampleCNs	Non-documented_objects
sampleCNs.AbstractCBS	Non-documented_objects
sampleName	Non-documented_objects
sampleName,AbstractCBS-method	getSampleName.AbstractCBS
sampleName.AbstractCBS	getSampleName.AbstractCBS
sampleName<-	Non-documented_objects
sampleName<-,AbstractCBS-method	setSampleName.AbstractCBS
sampleName<-.AbstractCBS	setSampleName.AbstractCBS
save,AbstractCBS-method	save.AbstractCBS
save.AbstractCBS	save.AbstractCBS
segmentByCBS	segmentByCBS
segmentByCBS.CBS	segmentByCBS
segmentByCBS.CNA	segmentByCBS
segmentByCBS.data.frame	segmentByCBS
segmentByCBS.default	segmentByCBS
segmentByNonPairedPSCBS	segmentByNonPairedPSCBS
segmentByNonPairedPSCBS.data.frame	segmentByNonPairedPSCBS
segmentByNonPairedPSCBS.default	segmentByNonPairedPSCBS
segmentByNonPairedPSCBS.PairedPSCBS	segmentByNonPairedPSCBS
segmentByPairedPSCBS	segmentByPairedPSCBS
segmentByPairedPSCBS.data.frame	segmentByPairedPSCBS
segmentByPairedPSCBS.default	segmentByPairedPSCBS
segmentByPairedPSCBS.PairedPSCBS	segmentByPairedPSCBS
seqOfSegmentsByDP	Non-documented_objects
seqOfSegmentsByDP.AbstractCBS	Non-documented_objects
seqOfSegmentsByDP.CBS	Non-documented_objects
seqOfSegmentsByDP.matrix	Non-documented_objects
seqOfSegmentsByDP.PairedPSCBS	Non-documented_objects
setLocusData	Non-documented_objects
setLocusData,AbstractCBS-method	getLocusData.AbstractCBS
setLocusData.AbstractCBS	getLocusData.AbstractCBS
setMeanEstimators	Non-documented_objects
setMeanEstimators.AbstractCBS	Non-documented_objects
setPloidy	ploidy.AbstractCBS
setPloidy,AbstractCBS-method	ploidy.AbstractCBS
setPloidy.AbstractCBS	ploidy.AbstractCBS
setSampleName	Non-documented_objects
setSampleName,AbstractCBS-method	setSampleName.AbstractCBS
setSampleName.AbstractCBS	setSampleName.AbstractCBS
setSegments	Non-documented_objects
setSegments,AbstractCBS-method	getSegments.AbstractCBS
setSegments.AbstractCBS	getSegments.AbstractCBS
shiftTCN	Non-documented_objects
shiftTCN.AbstractCBS	Non-documented_objects
shiftTCN.CBS	Non-documented_objects
shiftTCN.PairedPSCBS	Non-documented_objects
signalType	Non-documented_objects
signalType.CBS	Non-documented_objects
signalType<-	Non-documented_objects
signalType<-.CBS	Non-documented_objects
subset.CBS	Non-documented_objects
testROH	Non-documented_objects
testROH.numeric	testROH.numeric
tileChromosomes	Non-documented_objects
tileChromosomes.AbstractCBS	Non-documented_objects
tileChromosomes.CBS	Non-documented_objects
tileChromosomes.PairedPSCBS	Non-documented_objects
unTumorBoost	Non-documented_objects
unTumorBoost.PairedPSCBS	Non-documented_objects
updateBoundaries	Non-documented_objects
updateBoundaries.CBS	Non-documented_objects
updateMeans	Non-documented_objects
updateMeans,AbstractCBS-method	updateMeans.AbstractCBS
updateMeans.AbstractCBS	updateMeans.AbstractCBS
updateMeans.CBS	updateMeans.AbstractCBS
updateMeans.NonPairedPSCBS	updateMeans.AbstractCBS
updateMeans.PairedPSCBS	updateMeans.AbstractCBS
updateMeansC1C2	Non-documented_objects
updateMeansC1C2.PairedPSCBS	Non-documented_objects
updateMeansTogether	Non-documented_objects
updateMeansTogether,AbstractCBS-method	updateMeansTogether.AbstractCBS
updateMeansTogether.AbstractCBS	updateMeansTogether.AbstractCBS
updateMeansTogether.CBS	updateMeansTogether.AbstractCBS
updateMeansTogether.PairedPSCBS	updateMeansTogether.AbstractCBS
weightedQuantile	weightedQuantile
weightedQuantile.default	weightedQuantile
writeLocusData	Non-documented_objects
writeLocusData.CBS	Non-documented_objects
writeSegments	Non-documented_objects
writeSegments,CBS-method	writeSegments.CBS
writeSegments,PSCBS-method	writeSegments.PSCBS
writeSegments.CBS	writeSegments.CBS
writeSegments.DNAcopy	Non-documented_objects
writeSegments.PSCBS	writeSegments.PSCBS
writeWIG	writeSegments.CBS
writeWIG.AbstractCBS	writeSegments.CBS
