 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 normalizePrincipalCurve.matrix 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
clearCache.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

