 as.character.MultiSourceCopyNumberNormalization
  extractTupleOfDataFiles fitOne getAllNames
  getAsteriskTags.TotalCnSmoothing getFitAromaUgpFile getInputDataSets
  getOutputDataSets
  getOutputDataSets.MultiSourceCopyNumberNormalization
  getOutputFiles.TotalCnSmoothing getOutputPaths
  getOutputPaths.MultiSourceCopyNumberNormalization
  getParameters.MultiSourceCopyNumberNormalization
  getParameters.TotalCnSmoothing
  getParametersAsString.MultiSourceCopyNumberNormalization
  getPath.TotalCnSmoothing getRootPath.TotalCnSmoothing
  getSmoothedDataSets getSubsetToFit getTargetPositions
  getTargetPositions.TotalCnSmoothing getTargetUgpFile
  getTargetUgpFile.TotalCnSmoothing makeSmoothSplinePredict
  makeSmoothSplinePredict.numeric nbrOfDataSets
  nbrOfDataSets.MultiSourceCopyNumberNormalization normalizeOne
  normalizeOne.MultiSourceCopyNumberNormalization
  normalizePrincipalCurve pairs2
  pairs2.principal.curve process.TotalCnSmoothing
  getAsteriskTags.TotalCnKernelSmoothing
  getParameters.TotalCnKernelSmoothing smoothRawCopyNumbers
  smoothRawCopyNumbers.TotalCnKernelSmoothing
  smoothRawCopyNumbers.TotalCnSmoothing
  asCartesianSnpData asCartesianSnpData.CartesianSnpData
  asCartesianSnpData.PolarSnpData asCartesianSnpData.TotalFracBSnpData
  asPolarSnpData asPolarSnpData.CartesianSnpData
  asPolarSnpData.PolarSnpData asPolarSnpData.TotalFracBSnpData
  asTotalFracBSnpData asTotalFracBSnpData.CartesianSnpData
  asTotalFracBSnpData.PolarSnpData
  asTotalFracBSnpData.TotalFracBSnpData callGenotypes
  callGenotypes.SnpData callGenotypes.TotalFracBSnpData
  CartesianSnpData 
  pairedBoost pairedBoost.CartesianSnpData pairedBoost.PolarSnpData
  pairedBoost.TotalFracBSnpData plot.CartesianSnpData plot.PolarSnpData
  plot.SnpData plot.TotalFracBSnpData PolarSnpData SnpData
  TotalFracBSnpData
 as.character.TumorBoostNormalization getDataSets
 getDataSets.TumorBoostNormalization
 getInputDataSet.TumorBoostNormalization getNormalDataSet
 getNormalDataSet.TumorBoostNormalization getNormalGenotypeCallSet
 getNormalGenotypeCallSet.TumorBoostNormalization
 getOutputDataSet.TumorBoostNormalization getOutputPath
 getOutputPath.TumorBoostNormalization
 getRootPath.TumorBoostNormalization
 nbrOfFiles.TumorBoostNormalization process.TumorBoostNormalization
 getAsteriskTags.TumorBoostNormalization
 getFullName.TumorBoostNormalization getName.TumorBoostNormalization
 getPath.TumorBoostNormalization getTags.TumorBoostNormalization
 setTags.TumorBoostNormalization
 getAsteriskTags.MultiSourceCopyNumberNormalization
 getTags.MultiSourceCopyNumberNormalization
  getFlavor getFlavor.TumorBoostNormalization
  as.character.AbstractCurveNormalization backtransformOne
  backtransformOne.AbstractCurveNormalization
  backtransformOne.PrincipalCurveNormalization
  backtransformOne.XYCurveNormalization
  fitOne.AbstractCurveNormalization fitOne.PrincipalCurveNormalization
  fitOne.XYCurveNormalization
  getAsteriskTags.AbstractCurveNormalization
  getDataSets.AbstractCurveNormalization
  getFullName.AbstractCurveNormalization
  getInputDataSet.AbstractCurveNormalization
  getName.AbstractCurveNormalization
  getOutputDataSet.AbstractCurveNormalization
  getPairedDataSet.AbstractCurveNormalization
  getPath.AbstractCurveNormalization
  getRootPath.AbstractCurveNormalization
  getSubsetToFit.AbstractCurveNormalization
  getTags.AbstractCurveNormalization
  getTargetDataSet.AbstractCurveNormalization
  nbrOfFiles.AbstractCurveNormalization
  process.AbstractCurveNormalization setTags.AbstractCurveNormalization
  getSubsetToFit.PrincipalCurveNormalization
getPairedDataSet getTargetDataSet
  callGenotypes callGenotypes.RawAlleleBFractions getCalls
  getCalls.RawGenotypeCalls getColors getColors.RawGenotypeCalls
  isHeterozygous.RawGenotypeCalls isHomozygous.RawGenotypeCalls
  RawGenotypeCalls 
 normalizeTumorBoost.RawAlleleBFractions
  plotSmoothedPairsOne
  plotSmoothedPairsOne.MultiSourceCopyNumberNormalization
  getBacktransforms getBacktransforms.PrincipalCurve
  getPrincipalCurveEstimator
  getPrincipalCurveEstimator.MultiSourceCopyNumberNormalization
  plotBacktransforms plotBacktransforms.PrincipalCurve
  getDataSet getDataSet.NaiveFracBGenotyping getGenotypeCallSet
  getGenotypeCallSet.NaiveFracBGenotyping NaiveFracBGenotyping
  nbrOfLoci.NaiveFracBGenotyping nbrOfSNPs
  nbrOfSNPs.NaiveFracBGenotyping process.NaiveFracBGenotyping
  processOne processOne.NaiveFracBGenotyping segmentByPruneCBS
  segmentByPruneCBS.RawGenomicSignals
normalizeBAFsByRegions
  callAllelicBalanceByBAFs
  callCopyNeutralRegions 
  getXScale.CopyNumberRegions getYScale.CopyNumberRegions
  plot.CopyNumberRegions segmentByPruneCBSv1
  segmentByPruneCBSv1.RawGenomicSignals
orthogonalizeC1C2
  ABtoC1C2 bootstrap bootstrap.PairedPSCBS C1C2toAB deShearC1C2
  extractC1C2 extractC1C2.list fitLoess2D
  fitLoess2D.C1C2 fitLoessKD fitLoessKD.data.frame fitLoessKD.matrix
  normalizeLoess2D normalizeLoess2D.C1C2 normalizeLoessKD
  normalizeLoessKD.data.frame normalizeLoessKD.matrix plot.C1C2
  points.C1C2 resampleA resampleA.PairedPSCBS resampleB
  resampleB.PairedPSCBS resampleC resampleC.PairedPSCBS
  callPeaks callPeaks.data.frame
  deShearC1C2_v0 deShearC1C2_v0.PairedPSCBS extractDeltaC1C2
  extractDeltaC1C2.PairedPSCBS extractPolarDeltaC1C2
  extractPolarDeltaC1C2.PairedPSCBS fitC1C2ShearModel
  fitC1C2ShearModel.PairedPSCBS
 fitDeltaC1C2ShearModel fitDeltaC1C2ShearModel.PairedPSCBS
 fitDeltaXYShearModel fitDeltaXYShearModel.matrix
  calibrateC1C2 estimateC2Bias estimateC2Bias.PairedPSCBS
  fitC1C2Densities fitC1C2Densities.PairedPSCBS fitC1C2Peaks
  fitC1C2Peaks.PairedPSCBS plotC1C2Grid plotC1C2Grid.PairedPSCBS
  translateC1C2 translateC1C2.PairedPSCBS
transformC1C2 transformC1C2.PairedPSCBS
 PairedPSCBSFile PairedPSCBSFileSet byName.PairedPSCBSFileSet
 byPath.PairedPSCBSFileSet
 findAtomicAberrations.PairedPSCBS findByName.PairedPSCBSFileSet
 loadObject.PairedPSCBSFile
 plotTracks plotTracks.PruneCNA
 pruneCNA pruneCNA.PairedPSCBS
 testEqualityC1C2ByChiSquare testEqualityC1C2ByMean
 testEqualityTcnByMean testEqualityTcnByT 
cat getOption
drawC1C2Density drawC1C2Density.PairedPSCBS
getAsteriskTags.TotalCnBinnedSmoothing
getParameters.TotalCnBinnedSmoothing
smoothRawCopyNumbers.TotalCnBinnedSmoothing
findAtomicAberrations.CBS pruneCNA.AbstractCBS
[.PruneCNA extractGenerations extractGenerations.PruneCNA
findAtomicAberrations.CBS nbrOfGenerations
nbrOfGenerations.PruneCNA pruneCNA.AbstractCBS
testEqualityC1C2ByChiSq testEqualityC1orC2ByT
as.character.PairedPscbsModel
fit.PairedPscbsModel getAsteriskTags.PairedPscbsModel
getChipType.PairedPscbsModel getChromosomes.PairedPscbsModel
getDataSets.PairedPscbsModel getFitFunction.PairedPscbsModel
getFullName.PairedPscbsModel getName.PairedPscbsModel
getNormalDataSet.PairedPscbsModel
getOptionalArguments.PairedPscbsModel
getParameters.PairedPscbsModel
getParametersAsString.PairedPscbsModel getPath.PairedPscbsModel
getRandomSeed.PairedPscbsModel getRootPath.PairedPscbsModel
getTags.PairedPscbsModel getTumorDataSet
getTumorDataSet.PairedPscbsModel indexOf.PairedPscbsModel
nbrOfFiles.PairedPscbsModel setRandomSeed.PairedPscbsModel
setTags.PairedPscbsModel
calculatePairedPSCNByGenotype
calculatePairedPSCNByGenotype.data.frame
calculatePairedPSCNByGenotype.numeric
calculateTumorPSCNByGenotypeUsingCTCN
calculateTumorPSCNByGenotypeUsingCTCN.numeric
PairedPscbsCaller getAsteriskTags.PairedPscbsCaller
getParameters.PairedPscbsCaller getPath.PairedPscbsCaller
getPlatform.PairedPscbsCaller getRootPath.PairedPscbsCaller
process.PairedPscbsCaller
getOutputDataSet.PairedPscbsModel loadFit.PairedPSCBSFile
getChipType.PairedPSCBSFileSet
getDefaultFullName.PairedPSCBSFileSet
getPlatform.PairedPSCBSFileSet
getOptionalArguments.PairedPscbsCaller
backgroundCorrect backgroundCorrect.PairedPSCBS
getOutputDataSet0.TotalCnSmoothing getOutputFileClass
getOutputFileClass.TotalCnSmoothing getOutputFileExtension
getOutputFileExtension.TotalCnSmoothing getOutputFileSetClass
getOutputFileSetClass.TotalCnSmoothing
