 append append.PSCBS append.default arrowsC1C2 arrowsC1C2.PairedPSCBS
 arrowsDeltaC1C2 arrowsDeltaC1C2.PairedPSCBS as.data.frame.PairedPSCBS
 bootstrapCIs bootstrapCIs.PairedPSCBS bootstrapDHByRegion
 bootstrapDHByRegion.PairedPSCBS callABandHighAI
 callABandHighAI.PairedPSCBS 
 callExtremeAllelicImbalance
 callExtremeAllelicImbalance.PairedPSCBS callSegments
 callSegments.PairedPSCBS drawLevels drawLevels.DNAcopy
 drawLevels.PairedPSCBS extractByChromosome extractByChromosome.PSCBS
 extractC1C2 extractC1C2.PairedPSCBS extractDeltaC1C2
 extractDeltaC1C2.PairedPSCBS extractMinorMajorCNs
 extractMinorMajorCNs.PairedPSCBS extractTCNAndDHs
 extractTCNAndDHs.PairedPSCBS getChromosomes getChromosomes.PSCBS
 linesC1C2 linesC1C2.PairedPSCBS linesDeltaC1C2
 linesDeltaC1C2.PairedPSCBS nbrOfChromosomes nbrOfChromosomes.PSCBS
 nbrOfSegments nbrOfSegments.PSCBS plot.PairedPSCBS plotC1C2
 plotC1C2.PairedPSCBS plotDeltaC1C2 plotDeltaC1C2.PairedPSCBS
 pointsC1C2 pointsC1C2.PairedPSCBS pointsDeltaC1C2
 pointsDeltaC1C2.PairedPSCBS postsegmentTCN postsegmentTCN.PairedPSCBS
 print.PairedPSCBS subsetByDhSegments subsetByDhSegments.PairedPSCBS
 plotTracksManyChromosomes plotTracksManyChromosomes.PairedPSCBS
 tileChromosomes tileChromosomes.PairedPSCBS
 callExtremeAllelicImbalanceByDH
 callExtremeAllelicImbalanceByDH.PairedPSCBS
  as.data.frame.CBS drawLevels.CBS getChromosomes.CBS
  nbrOfChromosomes.CBS plot.CBS plotTracksManyChromosomes.CBS
  tileChromosomes.CBS
  bootstrapTCNandDHByRegion bootstrapTCNandDHByRegion.PairedPSCBS
  joinSegments joinSegments.CBS
drawConfidenceBands drawConfidenceBands.PairedPSCBS
 extractByChromosomes extractByChromosomes.PSCBS
 dropSegmentationOutliers dropSegmentationOutliers.default
 callABandLowC1 callABandLowC1.PairedPSCBS callLowC1ByC1
 callLowC1ByC1.PairedPSCBS
  estimateStdDevForHeterozygousBAF
  estimateStdDevForHeterozygousBAF.PairedPSCBS extractByRegion
  extractByRegion.PairedPSCBS extractByRegions
  extractByRegions.PairedPSCBS
 mergeTwoSegments mergeTwoSegments.PairedPSCBS 
 updateMeans updateMeans.PairedPSCBS
 dropByRegions dropByRegions.PairedPSCBS
 extractLocusLevelC1C2 extractLocusLevelC1C2.PairedPSCBS
 extractLocusLevelTCN extractLocusLevelTCN.PairedPSCBS
 plotTracks2 plotTracks2.PairedPSCBS
estimateMeanForDH estimateMeanForDH.PairedPSCBS
applyByRegion applyByRegion.PairedPSCBS
  estimateHighDHQuantileAtAB estimateHighDHQuantileAtAB.PairedPSCBS
  estimateKappa estimateKappaByC1Density
  callAllelicBalance callAllelicBalanceByDH
estimateDeltaAB
estimateDeltaABBySmallDH
estimateDeltaLOH estimateDeltaLOHByMinC1ForNonAB
 callAB callAllelicBalance.default
callLOH
