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

Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.

AuthorHenrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut]
Date of publication2015-10-28 00:08:16
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseLGPL (>= 2.1)
Version1.6.1
http://www.aroma-project.org/, https://github.com/HenrikBengtsson/aroma.cn

View on CRAN

Man pages

AbstractCurveNormalization: The AbstractCurveNormalization class

aroma.cn-package: Package aroma.cn

callAllelicBalanceByBAFs.PairedPSCBS: Calls regions that are in allelic balance

callCopyNeutralRegions.PairedPSCBS: Calls regions that are copy neutral

callPeaks.PeaksAndValleys: Calls the peaks in peaks-and-valley estimates

callXXorXY.numeric: Calls XX or XY from ChrX allele B fractions of a normal...

cnr: Simple creation of a CopyNumberRegions object

extractTupleOfDataFiles.MultiSourceCopyNumberNormalization: Gets a list of data files for a particular name across...

findAtomicAberrations.CopyNumberRegions: Finds all possible atomic regions

fitOne.MultiSourceCopyNumberNormalization: Fits the multi-source model for one sample

getAllNames.MultiSourceCopyNumberNormalization: Gets the names of all unique samples across all sources

getFitAromaUgpFile.MultiSourceCopyNumberNormalization: Gets the UGP file specifying the common set of loci to...

getInputDataSets.MultiSourceCopyNumberNormalization: Gets the list of data sets to be normalized

getSmoothedDataSets.MultiSourceCopyNumberNormalization: Gets the data sets smoothed toward the UGP file

getSubsetToFit.MultiSourceCopyNumberNormalization: Gets subset of (smoothing) units for fitting the model

MultiSourceCopyNumberNormalization: The MultiSourceCopyNumberNormalization class

Non-documented_objects: Non-documented objects

normalizeBAFsByRegions.PairedPSCBS: Normalizes allele B fractions (BAFs) based on region-based...

normalizeMirroredBAFsByRegions.matrix: Normalizes region-level mirrored allele B fractions (mBAFs)

normalizePrincipalCurve.matrix: Normalizes data in K dimensions using principal curves

PairedPscbsModel: The PairedPscbsModel class

PrincipalCurveNormalization: The PrincipalCurveNormalization class

process.MultiSourceCopyNumberNormalization: Normalizes all samples

testAllelicBalanceByBAFs: Tests for allelic balance in a genomic region

TotalCnBinnedSmoothing: The TotalCnBinnedSmoothing class

TotalCnKernelSmoothing: The TotalCnKernelSmoothing class

TotalCnSmoothing: The abstract TotalCnSmoothing class

TumorBoostNormalization: The TumorBoostNormalization class

XYCurveNormalization: The XYCurveNormalization class

Functions

AbstractCurveNormalization Man page
ABtoC1C2 Man page
aroma.cn Man page
aroma.cn-package Man page
asCartesianSnpData Man page
asCartesianSnpData.CartesianSnpData Man page
asCartesianSnpData.PolarSnpData Man page
asCartesianSnpData.TotalFracBSnpData Man page
as.character.AbstractCurveNormalization Man page
as.character.MultiSourceCopyNumberNormalization Man page
as.character.PairedPscbsModel Man page
as.character.TumorBoostNormalization 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
C1C2toAB 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 Man page
callAllelicBalanceByBAFs,PairedPSCBS-method Man page
callCopyNeutralRegions Man page
callCopyNeutralRegions.PairedPSCBS Man page
callCopyNeutralRegions,PairedPSCBS-method Man page
callGenotypes Man page
callGenotypes.RawAlleleBFractions Man page
callGenotypes.SnpData Man page
callGenotypes.TotalFracBSnpData Man page
callPeaks Man page
callPeaks.data.frame Man page
callPeaks.PeaksAndValleys Man page
callPeaks,PeaksAndValleys-method Man page
callXXorXY Man page
callXXorXY.numeric Man page
CartesianSnpData Man page
cat Man page
cnr Man page
CopyNumberRegions.findAtomicAberrations Man page
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 Man page
extractTupleOfDataFiles,MultiSourceCopyNumberNormalization-metho Man page
findAtomicAberrations Man page
findAtomicAberrations.CBS Man page
findAtomicAberrations.CopyNumberRegions Man page
findAtomicAberrations,CopyNumberRegions-method Man page
findAtomicAberrations.PairedPSCBS Man page
findByName.PairedPSCBSFileSet Man page
findLargeGaps.AromaUgpFile Man page
findLargeGaps.AromaUnitPscnBinarySet 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.AbstractCurveNormalization Man page
fitOne.MultiSourceCopyNumberNormalization Man page
fitOne,MultiSourceCopyNumberNormalization-method Man page
fitOne.PrincipalCurveNormalization Man page
fitOne.XYCurveNormalization Man page
fit.PairedPscbsModel Man page
getAllNames Man page
getAllNames.MultiSourceCopyNumberNormalization Man page
getAllNames,MultiSourceCopyNumberNormalization-method 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 Man page
getFitAromaUgpFile,MultiSourceCopyNumberNormalization-method 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
getInputDataSets Man page
getInputDataSets.MultiSourceCopyNumberNormalization Man page
getInputDataSets,MultiSourceCopyNumberNormalization-method Man page
getInputDataSet.TumorBoostNormalization 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
getOutputDataSet0.TotalCnSmoothing Man page
getOutputDataSet.AbstractCurveNormalization Man page
getOutputDataSet.PairedPscbsModel Man page
getOutputDataSets Man page
getOutputDataSets.MultiSourceCopyNumberNormalization Man page
getOutputDataSet.TumorBoostNormalization 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
getOutputPaths Man page
getOutputPaths.MultiSourceCopyNumberNormalization Man page
getOutputPath.TumorBoostNormalization Man page
getPairedDataSet Man page
getPairedDataSet.AbstractCurveNormalization Man page
getParametersAsString.MultiSourceCopyNumberNormalization Man page
getParametersAsString.PairedPscbsModel 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
getPath.AbstractCurveNormalization Man page
getPath.PairedPscbsCaller Man page
getPath.PairedPscbsModel Man page
getPath.TotalCnSmoothing Man page
getPath.TumorBoostNormalization Man page
getPlatform.PairedPscbsCaller Man page
getPlatform.PairedPSCBSFileSet 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 Man page
getSmoothedDataSets,MultiSourceCopyNumberNormalization-method Man page
getSubsetToFit Man page
getSubsetToFit.AbstractCurveNormalization Man page
getSubsetToFit.MultiSourceCopyNumberNormalization Man page
getSubsetToFit,MultiSourceCopyNumberNormalization-method 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
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
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
Non-documented objects Man page
normalizeBAFsByRegions Man page
normalizeBAFsByRegions.PairedPSCBS Man page
normalizeBAFsByRegions,PairedPSCBS-method 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
PairedPSCBS.callAllelicBalanceByBAFs Man page
PairedPSCBS.callCopyNeutralRegions Man page
PairedPscbsCaller Man page
PairedPSCBSFile Man page
PairedPSCBSFileSet Man page
PairedPscbsModel Man page
PairedPSCBS.normalizeBAFsByRegions Man page
pairs2 Man page
pairs2.principal.curve Man page
PeaksAndValleys.callPeaks Man page
plotBacktransforms Man page
plotBacktransforms.PrincipalCurve Man page
plot.C1C2 Man page
plotC1C2Grid Man page
plotC1C2Grid.PairedPSCBS Man page
plot.CartesianSnpData Man page
plot.CopyNumberRegions Man page
plot.PolarSnpData Man page
plotSmoothedPairsOne Man page
plotSmoothedPairsOne.MultiSourceCopyNumberNormalization Man page
plot.SnpData Man page
plot.TotalFracBSnpData Man page
plotTracks Man page
plotTracks.PruneCNA Man page
points.C1C2 Man page
PolarSnpData Man page
PrincipalCurveNormalization Man page
process.AbstractCurveNormalization Man page
process.MultiSourceCopyNumberNormalization Man page
process,MultiSourceCopyNumberNormalization-method Man page
process.NaiveFracBGenotyping Man page
processOne Man page
processOne.NaiveFracBGenotyping Man page
process.PairedPscbsCaller Man page
process.TotalCnSmoothing Man page
process.TumorBoostNormalization Man page
pruneCNA Man page
[.PruneCNA Man page
pruneCNA.AbstractCBS Man page
pruneCNA.PairedPSCBS Man page
RawGenotypeCalls 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
SnpData Man page
testAllelicBalanceByBAFs Man page
testAllelicBalanceByBAFs.default Man page
testEqualityC1C2ByChiSq Man page
testEqualityC1C2ByChiSquare Man page
testEqualityC1C2ByMean Man page
testEqualityC1orC2ByT Man page
testEqualityTcnByMean Man page
testEqualityTcnByT Man page
TotalCnBinnedSmoothing Man page
TotalCnKernelSmoothing Man page
TotalCnSmoothing Man page
TotalFracBSnpData Man page
transformC1C2 Man page
transformC1C2.PairedPSCBS Man page
translateC1C2 Man page
translateC1C2.PairedPSCBS Man page
TumorBoostNormalization Man page
XYCurveNormalization Man page

Files

aroma.cn
aroma.cn/inst
aroma.cn/inst/CITATION
aroma.cn/inst/testScripts
aroma.cn/inst/testScripts/setup
aroma.cn/inst/testScripts/setup/01c.installAllPackages.R
aroma.cn/inst/testScripts/setup/spawnTests.sh
aroma.cn/inst/testScripts/setup/99a.cleanupRootDirectories.R
aroma.cn/inst/testScripts/setup/01a.downloadAllAnnotationData.R
aroma.cn/inst/testScripts/setup/01b.downloadAllRawDataSet.R
aroma.cn/inst/testScripts/devel
aroma.cn/inst/testScripts/devel/C1C2
aroma.cn/inst/testScripts/devel/C1C2/21.PairedPSCBS,deShear,report.R
aroma.cn/inst/testScripts/devel/C1C2/31.PairedPSCBS,DP,deShear.R
aroma.cn/inst/testScripts/system
aroma.cn/inst/testScripts/system/CopyNumberProfiles
aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100909a,findAtomicAberrations.Rex
aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100911a,TumorClonality.Rex
aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100911b,TumorClonality,lineage.Rex
aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100909b,NormalContamination.Rex
aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100912b,Saturation.Rex
aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100912a,SegmentationStdError.Rex
aroma.cn/inst/testScripts/system/segmentation
aroma.cn/inst/testScripts/system/segmentation/20091110,CBS.Rex
aroma.cn/inst/testScripts/system/MSLHN
aroma.cn/inst/testScripts/system/MSLHN/20091218,TCGA,MSLHCN.Rex
aroma.cn/inst/testScripts/system/pairedPSCN
aroma.cn/inst/testScripts/system/pairedPSCN/R
aroma.cn/inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R
aroma.cn/inst/testScripts/system/pairedPSCN/R/00.setup.R
aroma.cn/inst/testScripts/system/pairedPSCN/R/getTumorNormalPairs.R
aroma.cn/inst/testScripts/system/pairedPSCN/R/zzz.R
aroma.cn/inst/testScripts/system/pairedPSCN/genomicPlots.tex.rsp
aroma.cn/inst/testScripts/system/CurveNormalization,OV
aroma.cn/inst/testScripts/system/CurveNormalization,OV/test20090715a,waves.Rex
aroma.cn/inst/testScripts/system/tracks
aroma.cn/inst/testScripts/system/tracks/20091008,HCC1143,CRMAv2-dChip-GTC,plot.Rex
aroma.cn/inst/testScripts/system/tracks/utils.R
aroma.cn/inst/testScripts/system/tracks/20091010,TCGA,plot.Rex
aroma.cn/inst/testScripts/system/TumorBoost
aroma.cn/inst/testScripts/system/TumorBoost/test20090429b,TBN.Rex
aroma.cn/inst/testScripts/system/TumorBoost/test20090429c,TBN,plot.Rex
aroma.cn/inst/testScripts/system/TumorBoost/test20090429d,TBN,LOH,plot.Rex
aroma.cn/inst/testScripts/system/TumorBoost/test20090429a,NGC.Rex
aroma.cn/inst/testScripts/system/TumorBoost/test20090620a,NGC.Rex
aroma.cn/inst/testScripts/system/MultiPlatform
aroma.cn/inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,shifts.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20090209,TCGA,plot.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20090210,TCGA,MSCN,plot.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20090208,TCGA,MSCN.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20100102,TCGA,MSCN,mpCBS.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,weights.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,wCBS.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20090720,TCGA,MSCN,tracks.Rex
aroma.cn/inst/testScripts/system/CondSegmentation
aroma.cn/inst/testScripts/system/CondSegmentation/test20090927,TBN,plot.Rex
aroma.cn/inst/testScripts/system/CondSegmentation/test20091014,TBN,plot.Rex
aroma.cn/inst/testScripts/system/chipTypes
aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6
aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/normalizeLoess2D.PairedPSCBS.Rex
aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/calibrateC1C2.PairedPSCBS.Rex
aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/calibrateC1C2,20111026.Rex
aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/deShearC1C2.PairedPSCBS.Rex
aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/orthogonalizeC1C2.PairedPSCBS.Rex
aroma.cn/inst/templates
aroma.cn/inst/templates/rsp
aroma.cn/inst/templates/rsp/PairedPSCBS,deShear,report.tex.rsp
aroma.cn/inst/templates/rsp/natbib.bst
aroma.cn/inst/templates/rsp/bioinformatics-journals-abbr.bib
aroma.cn/tests
aroma.cn/tests/callAllelicBalanceByBAFs.PairedPSCBS.R
aroma.cn/tests/cnr.R
aroma.cn/NAMESPACE
aroma.cn/NEWS
aroma.cn/R
aroma.cn/R/principal.curve.pairs2.R aroma.cn/R/NaiveFracBGenotyping.R aroma.cn/R/CopyNumberRegions.findAtomicAberrations.R aroma.cn/R/021.dynamic_imports.R aroma.cn/R/TotalCnSmoothing.R aroma.cn/R/XYCurveNormalization.R aroma.cn/R/000.R aroma.cn/R/normalizePrincipalCurve.matrix.R aroma.cn/R/SnpData.R aroma.cn/R/PrincipalCurve.XTRAS.R aroma.cn/R/PairedPSCBS.PLOT3.R aroma.cn/R/CartesianSnpData.R aroma.cn/R/TotalCnKernelSmoothing.R aroma.cn/R/PairedPSCBS.backgroundCorrect.R aroma.cn/R/TumorBoostNormalization.R aroma.cn/R/PairedPscbsModel.R aroma.cn/R/AromaUnitPscnBinarySet.doSegmentByPairedPSCBS.R aroma.cn/R/999.DEPRECATED.R aroma.cn/R/RawGenotypeCalls.R aroma.cn/R/PairedPSCBS.BOOT.R aroma.cn/R/009.setup.R aroma.cn/R/PairedPSCBS.fitC1C2Peaks.R aroma.cn/R/PruneCNA.PLOT.R aroma.cn/R/MultiSourceCopyNumberNormalization.R aroma.cn/R/PruneCNA.EXTS.R aroma.cn/R/TotalCnBinnedSmoothing.R aroma.cn/R/PairedPscbsCaller.R aroma.cn/R/segmentByPruneCBS.R aroma.cn/R/RawAlleleBFractions.XTRAS.R aroma.cn/R/callXXorXY.numeric.R aroma.cn/R/CBS.findAtomicAberrations.R aroma.cn/R/PairedPSCBS.NORM.R aroma.cn/R/normalizeMirroredBAFsByRegions.R aroma.cn/R/PolarSnpData.R aroma.cn/R/PairedPSCBS.findAtomicAberrations.R aroma.cn/R/testEquality.R aroma.cn/R/TotalFracBSnpData.R aroma.cn/R/PairedPSCBS.CALL2.R aroma.cn/R/PairedPSCBSFileSet.R aroma.cn/R/PrincipalCurveNormalization.R aroma.cn/R/MultiSourceCopyNumberNormalization.XTRAS.R aroma.cn/R/006.fixVarArgs.R aroma.cn/R/cnr.R aroma.cn/R/calculatePairedPSCNByGenotype.R aroma.cn/R/pruneCNA.R aroma.cn/R/PeaksAndValleys.EXTS.R aroma.cn/R/testAllelicBalanceByBAFs.R aroma.cn/R/999.NonDocumentedObjects.R aroma.cn/R/999.package.R aroma.cn/R/fitLoessKD.matrix.R aroma.cn/R/PairedPSCBSFile.R aroma.cn/R/zzz.R aroma.cn/R/C1C2.R aroma.cn/R/AbstractCurveNormalization.R
aroma.cn/MD5
aroma.cn/DESCRIPTION
aroma.cn/man
aroma.cn/man/extractTupleOfDataFiles.MultiSourceCopyNumberNormalization.Rd aroma.cn/man/getInputDataSets.MultiSourceCopyNumberNormalization.Rd aroma.cn/man/XYCurveNormalization.Rd aroma.cn/man/PrincipalCurveNormalization.Rd aroma.cn/man/AbstractCurveNormalization.Rd aroma.cn/man/fitOne.MultiSourceCopyNumberNormalization.Rd aroma.cn/man/aroma.cn-package.Rd aroma.cn/man/getSubsetToFit.MultiSourceCopyNumberNormalization.Rd aroma.cn/man/normalizePrincipalCurve.matrix.Rd aroma.cn/man/cnr.Rd aroma.cn/man/TotalCnBinnedSmoothing.Rd aroma.cn/man/getSmoothedDataSets.MultiSourceCopyNumberNormalization.Rd aroma.cn/man/TotalCnKernelSmoothing.Rd aroma.cn/man/TumorBoostNormalization.Rd aroma.cn/man/callPeaks.PeaksAndValleys.Rd aroma.cn/man/getFitAromaUgpFile.MultiSourceCopyNumberNormalization.Rd aroma.cn/man/callCopyNeutralRegions.PairedPSCBS.Rd aroma.cn/man/process.MultiSourceCopyNumberNormalization.Rd aroma.cn/man/normalizeMirroredBAFsByRegions.matrix.Rd aroma.cn/man/callXXorXY.numeric.Rd aroma.cn/man/MultiSourceCopyNumberNormalization.Rd aroma.cn/man/normalizeBAFsByRegions.PairedPSCBS.Rd aroma.cn/man/testAllelicBalanceByBAFs.Rd aroma.cn/man/getAllNames.MultiSourceCopyNumberNormalization.Rd aroma.cn/man/findAtomicAberrations.CopyNumberRegions.Rd aroma.cn/man/PairedPscbsModel.Rd aroma.cn/man/callAllelicBalanceByBAFs.PairedPSCBS.Rd aroma.cn/man/Non-documented_objects.Rd aroma.cn/man/TotalCnSmoothing.Rd

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