API for PSCBS
Analysis of Parent-Specific DNA Copy Numbers

Global functions
.addC1C2WithStatitics	Source code
.addCACBWithStatitics	Source code
.onAttach	Source code
.onLoad	Source code
.prememoize	Source code
.setupCacheRootPath	Source code
.stop_if_not	Source code
.use	Source code
.wtd.quantile	Source code
AbstractCBS	Man page
AbstractCBS.adjustPloidyScale	Man page
AbstractCBS.as.data.frame	Man page
AbstractCBS.dropChangePoint	Man page
AbstractCBS.dropChangePoints	Man page
AbstractCBS.dropRegion	Man page
AbstractCBS.dropRegions	Man page
AbstractCBS.getChromosomes	Man page
AbstractCBS.getLocusData	Man page
AbstractCBS.getSampleName	Man page
AbstractCBS.getSegments	Man page
AbstractCBS.hclustCNs	Man page
AbstractCBS.mergeThreeSegments	Man page
AbstractCBS.mergeTwoSegments	Man page
AbstractCBS.nbrOfChangePoints	Man page
AbstractCBS.nbrOfChromosomes	Man page
AbstractCBS.nbrOfLoci	Man page
AbstractCBS.nbrOfSegments	Man page
AbstractCBS.normalizeTotalCNs	Man page
AbstractCBS.ploidy	Man page
AbstractCBS.ploidy<-	Man page
AbstractCBS.plotTracks	Man page
AbstractCBS.pruneByDP	Man page
AbstractCBS.pruneByHClust	Man page
AbstractCBS.report	Man page
AbstractCBS.resetSegments	Man page
AbstractCBS.sampleName	Man page
AbstractCBS.sampleName<-	Man page
AbstractCBS.setLocusData	Man page
AbstractCBS.setPloidy	Man page
AbstractCBS.setSampleName	Man page
AbstractCBS.setSegments	Man page
AbstractCBS.updateMeans	Man page
AbstractCBS.updateMeansTogether	Man page
CBS	Man page
CBS.as.DNAcopy	Man page
CBS.as.data.frame	Man page
CBS.c	Man page
CBS.callAmplifications	Man page
CBS.callGainsAndLosses	Man page
CBS.callOutliers	Man page
CBS.estimateStandardDeviation	Man page
CBS.extractSegmentMeansByLocus	Man page
CBS.getCallStatistics	Man page
CBS.getFGA	Man page
CBS.getFGG	Man page
CBS.getFGL	Man page
CBS.getFractionOfGenomeAltered	Man page
CBS.getFractionOfGenomeGained	Man page
CBS.getFractionOfGenomeLost	Man page
CBS.getSmoothLocusData	Man page
CBS.joinSegments	Man page
CBS.mergeNonCalledSegments	Man page
CBS.plotTracks	Man page
CBS.pruneBySdUndo	Man page
CBS.writeSegments	Man page
DNAcopy.as.CBS	Man page
Non-documented objects	Man page
NonPairedPSCBS	Man page
PSCBS	Man page
PSCBS-package	Man page
PSCBS.getSegments	Man page
PSCBS.writeSegments	Man page
PairedPSCBS	Man page
PairedPSCBS.bootstrapTCNandDHByRegion	Man page
PairedPSCBS.callAB	Man page
PairedPSCBS.callAllelicBalance	Man page
PairedPSCBS.callAllelicBalanceByDH	Man page
PairedPSCBS.callCopyNeutral	Man page
PairedPSCBS.callCopyNeutralByTCNofAB	Man page
PairedPSCBS.callGNL	Man page
PairedPSCBS.callGNLByTCNofAB	Man page
PairedPSCBS.callGNLByTCNofABv1	Man page
PairedPSCBS.callGainNeutralLoss	Man page
PairedPSCBS.callLOH	Man page
PairedPSCBS.callNTCN	Man page
PairedPSCBS.callROH	Man page
PairedPSCBS.estimateDeltaAB	Man page
PairedPSCBS.estimateDeltaABBySmallDH	Man page
PairedPSCBS.estimateDeltaCN	Man page
PairedPSCBS.estimateDeltaLOH	Man page
PairedPSCBS.estimateDeltaLOHByMinC1ForNonAB	Man page
PairedPSCBS.estimateKappa	Man page
PairedPSCBS.estimateKappaByC1Density	Man page
PairedPSCBS.extractC1C2	Man page
PairedPSCBS.extractMinorMajorCNs	Man page
PairedPSCBS.extractTCNAndDHs	Man page
PairedPSCBS.getBootstrapLocusSets	Man page
PairedPSCBS.mergeTwoSegments	Man page
PairedPSCBS.plotTracks	Man page
PairedPSCBS.plotTracks1	Man page
PairedPSCBS.plotTracks2	Man page
PairedPSCBS.plotTracksManyChromosomes	Man page
RestructPSCBS	Man page
Restructuring AbstractCBS objects	Man page
adjustPloidyScale	Man page
adjustPloidyScale,AbstractCBS-method	Man page
adjustPloidyScale.AbstractCBS	Man page
adjustPloidyScale.PairedPSCBS	Man page
all.equal.AbstractCBS	Man page
all.equal.CBS	Man page
applyByRegion	Man page
applyByRegion.PairedPSCBS	Man page
arrowsC1C2	Man page
arrowsC1C2.PairedPSCBS	Man page
arrowsDeltaC1C2	Man page
arrowsDeltaC1C2.PairedPSCBS	Man page
as.CBS	Man page
as.CBS,DNAcopy-method	Man page
as.CBS.DNAcopy	Man page
as.DNAcopy	Man page
as.DNAcopy,CBS-method	Man page
as.DNAcopy.CBS	Man page
as.character.CBS	Man page
as.data.frame,AbstractCBS-method	Man page
as.data.frame,CBS-method	Man page
as.data.frame.AbstractCBS	Man page
as.data.frame.CBS	Man page
as.data.frame.PSCBS	Man page
bootstrapCIs	Man page
bootstrapCIs.PairedPSCBS	Man page
bootstrapDHByRegion	Man page
bootstrapDHByRegion.PairedPSCBS	Man page
bootstrapSegmentsAndChangepoints	Man page
bootstrapSegmentsAndChangepoints.PairedPSCBS	Man page
bootstrapTCNandDHByRegion	Man page
bootstrapTCNandDHByRegion,PairedPSCBS-method	Man page
bootstrapTCNandDHByRegion.PairedPSCBS	Man page
c,CBS-method	Man page
c.CBS	Man page
c.PSCBS	Man page
calcStatsForCopyNeutralABs	Man page
calcStatsForCopyNeutralABs.PairedPSCBS	Man page
callAB	Man page
callAB,PairedPSCBS-method	Man page
callAB.PairedPSCBS	Man page
callABandHighAI	Man page
callABandHighAI.PairedPSCBS	Man page
callABandLowC1	Man page
callABandLowC1.PairedPSCBS	Man page
callAllelicBalance	Man page
callAllelicBalance,PairedPSCBS-method	Man page
callAllelicBalance.PairedPSCBS	Man page
callAllelicBalance.default	Man page
callAllelicBalanceByDH	Man page
callAllelicBalanceByDH,PairedPSCBS-method	Man page
callAllelicBalanceByDH.PairedPSCBS	Man page
callAmplifications	Man page
callAmplifications,CBS-method	Man page
callAmplifications.CBS	Man page
callArms	Man page
callArms.CBS	Man page
callCopyNeutral	Man page
callCopyNeutral,PairedPSCBS-method	Man page
callCopyNeutral.PairedPSCBS	Man page
callCopyNeutralByTCNofAB	Man page
callCopyNeutralByTCNofAB,PairedPSCBS-method	Man page
callCopyNeutralByTCNofAB.PairedPSCBS	Man page
callExtremeAllelicImbalanceByDH	Man page
callExtremeAllelicImbalanceByDH.PairedPSCBS	Man page
callGLAO	Man page
callGLAO.CBS	Man page
callGNL	Man page
callGNL,PairedPSCBS-method	Man page
callGNL.PairedPSCBS	Man page
callGNLByTCNofAB	Man page
callGNLByTCNofAB,PairedPSCBS-method	Man page
callGNLByTCNofAB.PairedPSCBS	Man page
callGNLByTCNofABv1	Man page
callGNLByTCNofABv1,PairedPSCBS-method	Man page
callGNLByTCNofABv1.PairedPSCBS	Man page
callGainNeutralLoss	Man page
callGainNeutralLoss,PairedPSCBS-method	Man page
callGainNeutralLoss.PairedPSCBS	Man page
callGainsAndLosses	Man page
callGainsAndLosses,CBS-method	Man page
callGainsAndLosses.CBS	Man page
callLOH	Man page
callLOH,PairedPSCBS-method	Man page
callLOH.PairedPSCBS	Man page
callLowC1ByC1	Man page
callLowC1ByC1.PairedPSCBS	Man page
callNTCN	Man page
callNTCN,PairedPSCBS-method	Man page
callNTCN.PairedPSCBS	Man page
callOutliers	Man page
callOutliers,CBS-method	Man page
callOutliers.CBS	Man page
callROH	Man page
callROH,PairedPSCBS-method	Man page
callROH.NonPairedPSCBS	Man page
callROH.PairedPSCBS	Man page
callROHOneSegment	Man page
callROHOneSegment.PairedPSCBS	Man page
callSegmentationOutliers	Man page
callSegmentationOutliers.data.frame	Man page
callSegmentationOutliers.default	Man page
clearBootstrapSummaries	Man page
clearBootstrapSummaries.PairedPSCBS	Man page
clearCalls	Man page
clearCalls.AbstractCBS	Man page
drawCentromeres	Man page
drawCentromeres.CBS	Man page
drawChangePoints	Man page
drawChangePoints.AbstractCBS	Man page
drawChangePoints.CBS	Man page
drawChangePoints.PSCBS	Man page
drawChangePointsC1C2	Man page
drawChangePointsC1C2.PairedPSCBS	Man page
drawChromosomes	Man page
drawChromosomes.CBS	Man page
drawConfidenceBands	Man page
drawConfidenceBands.PairedPSCBS	Man page
drawKnownSegments	Man page
drawKnownSegments.AbstractCBS	Man page
drawLevels	Man page
drawLevels.CBS	Man page
drawLevels.DNAcopy	Man page
drawLevels.PairedPSCBS	Man page
dropChangePoint	Man page
dropChangePoint,AbstractCBS-method	Man page
dropChangePoint.AbstractCBS	Man page
dropChangePoints	Man page
dropChangePoints,AbstractCBS-method	Man page
dropChangePoints.AbstractCBS	Man page
dropRegion	Man page
dropRegion,AbstractCBS-method	Man page
dropRegion.AbstractCBS	Man page
dropRegions	Man page
dropRegions,AbstractCBS-method	Man page
dropRegions.AbstractCBS	Man page
dropSegmentationOutliers	Man page
dropSegmentationOutliers.data.frame	Man page
dropSegmentationOutliers.default	Man page
encodeCalls	Man page
encodeCalls.data.frame	Man page
estimateDeltaAB	Man page
estimateDeltaAB,PairedPSCBS-method	Man page
estimateDeltaAB.PairedPSCBS	Man page
estimateDeltaABBySmallDH	Man page
estimateDeltaABBySmallDH,PairedPSCBS-method	Man page
estimateDeltaABBySmallDH.PairedPSCBS	Man page
estimateDeltaCN	Man page
estimateDeltaCN,PairedPSCBS-method	Man page
estimateDeltaCN.CBS	Man page
estimateDeltaCN.PairedPSCBS	Man page
estimateDeltaLOH	Man page
estimateDeltaLOH,PairedPSCBS-method	Man page
estimateDeltaLOH.PairedPSCBS	Man page
estimateDeltaLOHByMinC1ForNonAB	Man page
estimateDeltaLOHByMinC1ForNonAB,PairedPSCBS-method	Man page
estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS	Man page
estimateHighDHQuantileAtAB	Man page
estimateHighDHQuantileAtAB.PairedPSCBS	Man page
estimateKappa	Man page
estimateKappa,PairedPSCBS-method	Man page
estimateKappa.PairedPSCBS	Man page
estimateKappaByC1Density	Man page
estimateKappaByC1Density,PairedPSCBS-method	Man page
estimateKappaByC1Density.PairedPSCBS	Man page
estimateMeanForDH	Man page
estimateMeanForDH.PairedPSCBS	Man page
estimateStandardDeviation	Man page
estimateStandardDeviation,CBS-method	Man page
estimateStandardDeviation.CBS	Man page
estimateStandardDeviation.DNAcopy	Man page
estimateStdDevForHeterozygousBAF	Man page
estimateStdDevForHeterozygousBAF.PairedPSCBS	Man page
exampleData	Man page
exampleData.default	Man page
extractC1C2	Man page
extractC1C2,PairedPSCBS-method	Man page
extractC1C2.PairedPSCBS	Man page
extractCNs	Man page
extractCNs.AbstractCBS	Man page
extractCNs.CBS	Man page
extractCNs.PairedPSCBS	Man page
extractCallsByLocus	Man page
extractCallsByLocus.CBS	Man page
extractCallsByLocus.PairedPSCBS	Man page
extractChromosome	Man page
extractChromosome.AbstractCBS	Man page
extractChromosomes	Man page
extractChromosomes.AbstractCBS	Man page
extractChromosomes.CBS	Man page
extractChromosomes.PSCBS	Man page
extractDeltaC1C2	Man page
extractDeltaC1C2.PairedPSCBS	Man page
extractDhSegment	Man page
extractDhSegment.PairedPSCBS	Man page
extractLocusLevelC1C2	Man page
extractLocusLevelC1C2.PairedPSCBS	Man page
extractLocusLevelTCN	Man page
extractLocusLevelTCN.PairedPSCBS	Man page
extractMinorMajorCNs	Man page
extractMinorMajorCNs,PairedPSCBS-method	Man page
extractMinorMajorCNs.PairedPSCBS	Man page
extractRegion	Man page
extractRegion.AbstractCBS	Man page
extractRegions	Man page
extractRegions.AbstractCBS	Man page
extractSegment	Man page
extractSegment.AbstractCBS	Man page
extractSegmentDataByLocus	Man page
extractSegmentDataByLocus.PairedPSCBS	Man page
extractSegmentMeansByLocus	Man page
extractSegmentMeansByLocus,CBS-method	Man page
extractSegmentMeansByLocus.CBS	Man page
extractSegmentMeansByLocus.DNAcopy	Man page
extractSegments	Man page
extractSegments.AbstractCBS	Man page
extractSegments.CBS	Man page
extractSegments.PairedPSCBS	Man page
extractTCNAndDHs	Man page
extractTCNAndDHs,PairedPSCBS-method	Man page
extractTCNAndDHs.PairedPSCBS	Man page
extractTotalCNs	Man page
extractTotalCNs.CBS	Man page
extractWIG	Man page
extractWIG.AbstractCBS	Man page
extractWIG.CBS	Man page
extractWIG.PSCBS	Man page
findBootstrapSummaries	Man page
findBootstrapSummaries.PairedPSCBS	Man page
findLargeGaps	Man page
findLargeGaps.data.frame	Man page
findLargeGaps.default	Man page
findNeutralCopyNumberState	Man page
findNeutralCopyNumberState.default	Man page
gapsToSegments	Man page
gapsToSegments.data.frame	Man page
getBootstrapLocusSets	Man page
getBootstrapLocusSets,PairedPSCBS-method	Man page
getBootstrapLocusSets.PairedPSCBS	Man page
getCallStatistics	Man page
getCallStatistics,CBS-method	Man page
getCallStatistics.CBS	Man page
getCallStatisticsByArms	Man page
getCallStatisticsByArms.CBS	Man page
getChangePoints	Man page
getChangePoints.AbstractCBS	Man page
getChangePoints.CBS	Man page
getChangePoints.PSCBS	Man page
getChromosomeOffsets	Man page
getChromosomeOffsets.AbstractCBS	Man page
getChromosomeOffsets.PairedPSCBS	Man page
getChromosomeRanges	Man page
getChromosomeRanges.AbstractCBS	Man page
getChromosomeRanges.CBS	Man page
getChromosomeRanges.PairedPSCBS	Man page
getChromosomes	Man page
getChromosomes,AbstractCBS-method	Man page
getChromosomes.AbstractCBS	Man page
getChromosomes.DNAcopy	Man page
getFGA	Man page
getFGA,CBS-method	Man page
getFGA.CBS	Man page
getFGG	Man page
getFGG,CBS-method	Man page
getFGG.CBS	Man page
getFGL	Man page
getFGL,CBS-method	Man page
getFGL.CBS	Man page
getFractionOfGenomeAltered	Man page
getFractionOfGenomeAltered,CBS-method	Man page
getFractionOfGenomeAltered.CBS	Man page
getFractionOfGenomeGained	Man page
getFractionOfGenomeGained,CBS-method	Man page
getFractionOfGenomeGained.CBS	Man page
getFractionOfGenomeLost	Man page
getFractionOfGenomeLost,CBS-method	Man page
getFractionOfGenomeLost.CBS	Man page
getLocusData	Man page
getLocusData,AbstractCBS-method	Man page
getLocusData.AbstractCBS	Man page
getLocusData.CBS	Man page
getLocusData.NonPairedPSCBS	Man page
getLocusData.PSCBS	Man page
getLocusData.PairedPSCBS	Man page
getLocusSignalNames	Man page
getLocusSignalNames.AbstractCBS	Man page
getLocusSignalNames.CBS	Man page
getLocusSignalNames.PSCBS	Man page
getMeanEstimators	Man page
getMeanEstimators.AbstractCBS	Man page
getSampleName	Man page
getSampleName,AbstractCBS-method	Man page
getSampleName.AbstractCBS	Man page
getSampleNames	Man page
getSampleNames.DNAcopy	Man page
getSegmentSizes	Man page
getSegmentSizes.AbstractCBS	Man page
getSegmentSizes.CBS	Man page
getSegmentSizes.PSCBS	Man page
getSegmentTrackPrefixes	Man page
getSegmentTrackPrefixes.AbstractCBS	Man page
getSegmentTrackPrefixes.CBS	Man page
getSegmentTrackPrefixes.PSCBS	Man page
getSegments	Man page
getSegments,AbstractCBS-method	Man page
getSegments,PSCBS-method	Man page
getSegments.AbstractCBS	Man page
getSegments.CBS	Man page
getSegments.PSCBS	Man page
getSignalType	Man page
getSignalType.CBS	Man page
getSmoothLocusData	Man page
getSmoothLocusData,CBS-method	Man page
getSmoothLocusData.CBS	Man page
hasBootstrapSummaries	Man page
hasBootstrapSummaries.PairedPSCBS	Man page
hclustCNs	Man page
hclustCNs,AbstractCBS-method	Man page
hclustCNs.AbstractCBS	Man page
highlightArmCalls	Man page
highlightArmCalls.CBS	Man page
highlightCalls	Man page
highlightCalls.CBS	Man page
highlightLocusCalls	Man page
highlightLocusCalls.CBS	Man page
installDNAcopy	Man page
installDNAcopy.default	Man page
isLocallyPhased	Man page
isLocallyPhased.PSCBS	Man page
isSegmentSplitter	Man page
isSegmentSplitter.CBS	Man page
isSegmentSplitter.PSCBS	Man page
isWholeChromosomeGained	Man page
isWholeChromosomeGained.CBS	Man page
isWholeChromosomeLost	Man page
isWholeChromosomeLost.CBS	Man page
joinSegments	Man page
joinSegments,CBS-method	Man page
joinSegments.CBS	Man page
linesC1C2	Man page
linesC1C2.PairedPSCBS	Man page
linesDeltaC1C2	Man page
linesDeltaC1C2.PairedPSCBS	Man page
mergeNonCalledSegments	Man page
mergeNonCalledSegments,CBS-method	Man page
mergeNonCalledSegments.CBS	Man page
mergeThreeSegments	Man page
mergeThreeSegments,AbstractCBS-method	Man page
mergeThreeSegments.AbstractCBS	Man page
mergeTwoSegments	Man page
mergeTwoSegments,AbstractCBS-method	Man page
mergeTwoSegments,PairedPSCBS-method	Man page
mergeTwoSegments.AbstractCBS	Man page
mergeTwoSegments.CBS	Man page
mergeTwoSegments.PairedPSCBS	Man page
nbrOfAmplifications	Man page
nbrOfAmplifications.CBS	Man page
nbrOfChangePoints	Man page
nbrOfChangePoints,AbstractCBS-method	Man page
nbrOfChangePoints.AbstractCBS	Man page
nbrOfChromosomes	Man page
nbrOfChromosomes,AbstractCBS-method	Man page
nbrOfChromosomes.AbstractCBS	Man page
nbrOfGains	Man page
nbrOfGains.CBS	Man page
nbrOfLoci	Man page
nbrOfLoci,AbstractCBS-method	Man page
nbrOfLoci.AbstractCBS	Man page
nbrOfLoci.DNAcopy	Man page
nbrOfLosses	Man page
nbrOfLosses.CBS	Man page
nbrOfSamples	Man page
nbrOfSamples.DNAcopy	Man page
nbrOfSegments	Man page
nbrOfSegments,AbstractCBS-method	Man page
nbrOfSegments.AbstractCBS	Man page
nbrOfSegments.DNAcopy	Man page
normalizeTotalCNs	Man page
normalizeTotalCNs,AbstractCBS-method	Man page
normalizeTotalCNs.AbstractCBS	Man page
normalizeTotalCNs.PSCBS	Man page
ploidy	Man page
ploidy,AbstractCBS-method	Man page
ploidy.AbstractCBS	Man page
ploidy<-	Man page
ploidy<-,AbstractCBS-method	Man page
ploidy<-.AbstractCBS	Man page
plot	Man page
plot.CBS	Man page
plot.PairedPSCBS	Man page
plotC1C2	Man page
plotC1C2.PairedPSCBS	Man page
plotDeltaC1C2	Man page
plotDeltaC1C2.PairedPSCBS	Man page
plotTracks	Man page
plotTracks,AbstractCBS-method	Man page
plotTracks,CBS-method	Man page
plotTracks,PairedPSCBS-method	Man page
plotTracks.AbstractCBS	Man page
plotTracks.CBS	Man page
plotTracks.PairedPSCBS	Man page
plotTracks1	Man page
plotTracks1,PairedPSCBS-method	Man page
plotTracks1.PairedPSCBS	Man page
plotTracks2	Man page
plotTracks2,PairedPSCBS-method	Man page
plotTracks2.PairedPSCBS	Man page
plotTracksManyChromosomes	Man page
plotTracksManyChromosomes,PairedPSCBS-method	Man page
plotTracksManyChromosomes.CBS	Man page
plotTracksManyChromosomes.PairedPSCBS	Man page
pointsC1C2	Man page
pointsC1C2.PairedPSCBS	Man page
pointsDeltaC1C2	Man page
pointsDeltaC1C2.PairedPSCBS	Man page
postsegmentTCN	Man page
postsegmentTCN.PairedPSCBS	Man page
print.AbstractCBS	Man page
pruneByDP	Man page
pruneByDP,AbstractCBS-method	Man page
pruneByDP.AbstractCBS	Man page
pruneByHClust	Man page
pruneByHClust,AbstractCBS-method	Man page
pruneByHClust.AbstractCBS	Man page
pruneBySdUndo	Man page
pruneBySdUndo,CBS-method	Man page
pruneBySdUndo.CBS	Man page
randomSeed	Man page
renameChromosomes	Man page
renameChromosomes.AbstractCBS	Man page
report	Man page
report,AbstractCBS-method	Man page
report.AbstractCBS	Man page
resegment	Man page
resegment.AbstractCBS	Man page
resegment.CBS	Man page
resegment.NonPairedPSCBS	Man page
resegment.PairedPSCBS	Man page
resetSegments	Man page
resetSegments,AbstractCBS-method	Man page
resetSegments.AbstractCBS	Man page
sampleCNs	Man page
sampleCNs.AbstractCBS	Man page
sampleName	Man page
sampleName,AbstractCBS-method	Man page
sampleName.AbstractCBS	Man page
sampleName<-	Man page
sampleName<-,AbstractCBS-method	Man page
sampleName<-.AbstractCBS	Man page
segmentByCBS	Man page Man page
segmentByCBS.CBS	Man page
segmentByCBS.CNA	Man page
segmentByCBS.data.frame	Man page
segmentByCBS.default	Man page
segmentByNonPairedPSCBS	Man page Man page
segmentByNonPairedPSCBS.PairedPSCBS	Man page
segmentByNonPairedPSCBS.data.frame	Man page
segmentByNonPairedPSCBS.default	Man page
segmentByPairedPSCBS	Man page Man page
segmentByPairedPSCBS.PairedPSCBS	Man page
segmentByPairedPSCBS.data.frame	Man page
segmentByPairedPSCBS.default	Man page
seqOfSegmentsByDP	Man page
seqOfSegmentsByDP.AbstractCBS	Man page
seqOfSegmentsByDP.CBS	Man page
seqOfSegmentsByDP.PairedPSCBS	Man page
seqOfSegmentsByDP.matrix	Man page
setLocusData	Man page
setLocusData,AbstractCBS-method	Man page
setLocusData.AbstractCBS	Man page Man page
setMeanEstimators	Man page
setMeanEstimators.AbstractCBS	Man page
setPloidy	Man page
setPloidy,AbstractCBS-method	Man page
setPloidy.AbstractCBS	Man page
setSampleName	Man page
setSampleName,AbstractCBS-method	Man page
setSampleName.AbstractCBS	Man page
setSegments	Man page
setSegments,AbstractCBS-method	Man page
setSegments.AbstractCBS	Man page Man page
shiftTCN	Man page
shiftTCN.AbstractCBS	Man page
shiftTCN.CBS	Man page
shiftTCN.PairedPSCBS	Man page
signalType	Man page
signalType.CBS	Man page
signalType<-	Man page
signalType<-.CBS	Man page
subset.CBS	Man page
testROH	Man page
testROH.numeric	Man page
tileChromosomes	Man page
tileChromosomes.AbstractCBS	Man page
tileChromosomes.CBS	Man page
tileChromosomes.PairedPSCBS	Man page
unTumorBoost	Man page
unTumorBoost.PairedPSCBS	Man page
updateBoundaries	Man page
updateBoundaries.CBS	Man page
updateMeans	Man page
updateMeans,AbstractCBS-method	Man page
updateMeans.AbstractCBS	Man page
updateMeans.CBS	Man page
updateMeans.NonPairedPSCBS	Man page
updateMeans.PairedPSCBS	Man page
updateMeansC1C2	Man page
updateMeansC1C2.PairedPSCBS	Man page
updateMeansTogether	Man page
updateMeansTogether,AbstractCBS-method	Man page
updateMeansTogether.AbstractCBS	Man page
updateMeansTogether.CBS	Man page
updateMeansTogether.PairedPSCBS	Man page
weightedQuantile	Man page
weightedQuantile.default	Man page
writeLocusData	Man page
writeLocusData.CBS	Man page
writeSegments	Man page
writeSegments,CBS-method	Man page
writeSegments,PSCBS-method	Man page
writeSegments.CBS	Man page
writeSegments.DNAcopy	Man page
writeSegments.PSCBS	Man page
writeWIG	Man page
writeWIG.AbstractCBS	Man page