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