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 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.