API for aroma.cn
Copy-Number Analysis of Large Microarray Data Sets

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