Package: aroma.cn 1.7.1

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.

Authors:Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut]

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Bug tracker:https://github.com/henrikbengtsson/aroma.cn/issues

On CRAN:

293 exports 1 stars 0.95 score 22 dependencies 9 scripts 455 downloads

Last updated 7 months agofrom:df71918f6f (on master). Checks:OK: 6 WARNING: 1. Indexed: yes.

Exports:[.PruneCNAAbstractCurveNormalizationABtoC1C2aroma.cnas.character.AbstractCurveNormalizationas.character.MultiSourceCopyNumberNormalizationas.character.PairedPscbsModelas.character.TumorBoostNormalizationasCartesianSnpDataasCartesianSnpData.CartesianSnpDataasCartesianSnpData.PolarSnpDataasCartesianSnpData.TotalFracBSnpDataasPolarSnpDataasPolarSnpData.CartesianSnpDataasPolarSnpData.PolarSnpDataasPolarSnpData.TotalFracBSnpDataasTotalFracBSnpDataasTotalFracBSnpData.CartesianSnpDataasTotalFracBSnpData.PolarSnpDataasTotalFracBSnpData.TotalFracBSnpDatabackgroundCorrectbackgroundCorrect.PairedPSCBSbacktransformOnebacktransformOne.AbstractCurveNormalizationbacktransformOne.PrincipalCurveNormalizationbacktransformOne.XYCurveNormalizationbootstrapbootstrap.PairedPSCBSbyName.PairedPSCBSFileSetbyPath.PairedPSCBSFileSetC1C2toABcalculatePairedPSCNByGenotypecalculatePairedPSCNByGenotype.data.framecalculatePairedPSCNByGenotype.numericcalculateTumorPSCNByGenotypeUsingCTCNcalculateTumorPSCNByGenotypeUsingCTCN.numericcallAllelicBalanceByBAFscallAllelicBalanceByBAFs.PairedPSCBScallCopyNeutralRegionscallCopyNeutralRegions.PairedPSCBScallGenotypescallGenotypes.RawAlleleBFractionscallGenotypes.SnpDatacallGenotypes.TotalFracBSnpDatacallPeakscallPeaks.PeaksAndValleyscallXXorXYcallXXorXY.numericCartesianSnpDatacnrdoSegmentByPairedPSCBSdoSegmentByPairedPSCBS.AromaUnitPscnBinarySetdrawC1C2DensitydrawC1C2Density.PairedPSCBSestimateC2BiasestimateC2Bias.PairedPSCBSextractC1C2.listextractGenerationsextractGenerations.PruneCNAextractTupleOfDataFilesextractTupleOfDataFiles.MultiSourceCopyNumberNormalizationfindAtomicAberrationsfindAtomicAberrations.CBSfindAtomicAberrations.CopyNumberRegionsfindAtomicAberrations.PairedPSCBSfindByName.PairedPSCBSFileSetfindLargeGaps.AromaUgpFilefindLargeGaps.AromaUnitPscnBinarySetfit.PairedPscbsModelfitC1C2DensitiesfitC1C2Densities.PairedPSCBSfitC1C2PeaksfitC1C2Peaks.PairedPSCBSfitLoess2DfitLoess2D.C1C2fitLoessKDfitLoessKD.data.framefitLoessKD.matrixfitOnefitOne.AbstractCurveNormalizationfitOne.MultiSourceCopyNumberNormalizationfitOne.PrincipalCurveNormalizationfitOne.XYCurveNormalizationgetAllNamesgetAllNames.MultiSourceCopyNumberNormalizationgetAsteriskTags.AbstractCurveNormalizationgetAsteriskTags.MultiSourceCopyNumberNormalizationgetAsteriskTags.PairedPscbsCallergetAsteriskTags.PairedPscbsModelgetAsteriskTags.TotalCnBinnedSmoothinggetAsteriskTags.TotalCnKernelSmoothinggetAsteriskTags.TotalCnSmoothinggetAsteriskTags.TumorBoostNormalizationgetBacktransformsgetBacktransforms.PrincipalCurvegetCalls.RawGenotypeCallsgetChipType.PairedPSCBSFileSetgetChipType.PairedPscbsModelgetChromosomes.PairedPscbsModelgetColorsgetColors.RawGenotypeCallsgetDataSetgetDataSet.NaiveFracBGenotypinggetDataSetsgetDataSets.AbstractCurveNormalizationgetDataSets.PairedPscbsModelgetDataSets.TumorBoostNormalizationgetDefaultFullName.PairedPSCBSFileSetgetFitAromaUgpFilegetFitAromaUgpFile.MultiSourceCopyNumberNormalizationgetFitFunction.PairedPscbsModelgetFlavorgetFlavor.TumorBoostNormalizationgetFullName.AbstractCurveNormalizationgetFullName.PairedPscbsModelgetFullName.TumorBoostNormalizationgetGenotypeCallSetgetGenotypeCallSet.NaiveFracBGenotypinggetInputDataSet.AbstractCurveNormalizationgetInputDataSet.TumorBoostNormalizationgetInputDataSetsgetInputDataSets.MultiSourceCopyNumberNormalizationgetName.AbstractCurveNormalizationgetName.PairedPscbsModelgetName.TumorBoostNormalizationgetNormalDataSetgetNormalDataSet.PairedPscbsModelgetNormalDataSet.TumorBoostNormalizationgetNormalGenotypeCallSetgetNormalGenotypeCallSet.TumorBoostNormalizationgetOptionalArguments.PairedPscbsCallergetOptionalArguments.PairedPscbsModelgetOutputDataSet.AbstractCurveNormalizationgetOutputDataSet.PairedPscbsModelgetOutputDataSet.TumorBoostNormalizationgetOutputDataSet0.TotalCnSmoothinggetOutputDataSetsgetOutputDataSets.MultiSourceCopyNumberNormalizationgetOutputFileClassgetOutputFileClass.TotalCnSmoothinggetOutputFileExtensiongetOutputFileExtension.TotalCnSmoothinggetOutputFiles.TotalCnSmoothinggetOutputFileSetClassgetOutputFileSetClass.TotalCnSmoothinggetOutputPathsgetOutputPaths.MultiSourceCopyNumberNormalizationgetPairedDataSetgetPairedDataSet.AbstractCurveNormalizationgetParameters.MultiSourceCopyNumberNormalizationgetParameters.PairedPscbsCallergetParameters.PairedPscbsModelgetParameters.TotalCnBinnedSmoothinggetParameters.TotalCnKernelSmoothinggetParameters.TotalCnSmoothinggetPath.AbstractCurveNormalizationgetPath.PairedPscbsCallergetPath.PairedPscbsModelgetPath.TotalCnSmoothinggetPath.TumorBoostNormalizationgetPlatform.PairedPscbsCallergetPlatform.PairedPSCBSFileSetgetPrincipalCurveEstimatorgetPrincipalCurveEstimator.MultiSourceCopyNumberNormalizationgetRandomSeed.PairedPscbsModelgetRootPath.AbstractCurveNormalizationgetRootPath.PairedPscbsCallergetRootPath.PairedPscbsModelgetRootPath.TotalCnSmoothinggetRootPath.TumorBoostNormalizationgetSmoothedDataSetsgetSmoothedDataSets.MultiSourceCopyNumberNormalizationgetSubsetToFitgetSubsetToFit.AbstractCurveNormalizationgetSubsetToFit.MultiSourceCopyNumberNormalizationgetSubsetToFit.PrincipalCurveNormalizationgetTags.AbstractCurveNormalizationgetTags.MultiSourceCopyNumberNormalizationgetTags.PairedPscbsModelgetTags.TumorBoostNormalizationgetTargetDataSetgetTargetDataSet.AbstractCurveNormalizationgetTargetPositionsgetTargetPositions.TotalCnSmoothinggetTargetUgpFilegetTargetUgpFile.TotalCnSmoothinggetTumorDataSetgetTumorDataSet.PairedPscbsModelgetXScale.CopyNumberRegionsgetYScale.CopyNumberRegionsindexOf.PairedPscbsModelisHeterozygous.RawGenotypeCallsisHomozygous.RawGenotypeCallsloadFit.PairedPSCBSFileloadObject.PairedPSCBSFileMultiSourceCopyNumberNormalizationNaiveFracBGenotypingnbrOfDataSetsnbrOfDataSets.MultiSourceCopyNumberNormalizationnbrOfFiles.AbstractCurveNormalizationnbrOfFiles.PairedPscbsModelnbrOfFiles.TumorBoostNormalizationnbrOfGenerationsnbrOfGenerations.PruneCNAnbrOfLoci.NaiveFracBGenotypingnbrOfSNPsnbrOfSNPs.NaiveFracBGenotypingnormalizeBAFsByRegionsnormalizeBAFsByRegions.PairedPSCBSnormalizeLoess2DnormalizeLoess2D.C1C2normalizeLoessKDnormalizeLoessKD.data.framenormalizeLoessKD.matrixnormalizeMirroredBAFsByRegionsnormalizeMirroredBAFsByRegions.matrixnormalizeOnenormalizeOne.MultiSourceCopyNumberNormalizationnormalizePrincipalCurvenormalizePrincipalCurve.matrixnormalizeTumorBoost.RawAlleleBFractionspairedBoostpairedBoost.CartesianSnpDatapairedBoost.PolarSnpDatapairedBoost.TotalFracBSnpDataPairedPscbsCallerPairedPSCBSFilePairedPSCBSFileSetPairedPscbsModelpairs2pairs2.principal.curveplot.C1C2plot.CartesianSnpDataplot.CopyNumberRegionsplot.PolarSnpDataplot.TotalFracBSnpDataplotBacktransformsplotBacktransforms.PrincipalCurveplotC1C2GridplotC1C2Grid.PairedPSCBSplotSmoothedPairsOneplotSmoothedPairsOne.MultiSourceCopyNumberNormalizationplotTracks.PruneCNApoints.C1C2PolarSnpDataPrincipalCurveNormalizationprocess.AbstractCurveNormalizationprocess.MultiSourceCopyNumberNormalizationprocess.NaiveFracBGenotypingprocess.PairedPscbsCallerprocess.TotalCnSmoothingprocess.TumorBoostNormalizationprocessOneprocessOne.NaiveFracBGenotypingpruneCNApruneCNA.AbstractCBSRawGenotypeCallsresampleAresampleA.PairedPSCBSresampleBresampleB.PairedPSCBSresampleCresampleC.PairedPSCBSsegmentByPruneCBSsegmentByPruneCBS.RawGenomicSignalssegmentByPruneCBSv1segmentByPruneCBSv1.RawGenomicSignalssetRandomSeed.PairedPscbsModelsetTags.AbstractCurveNormalizationsetTags.PairedPscbsModelsetTags.TumorBoostNormalizationsmoothRawCopyNumberssmoothRawCopyNumbers.TotalCnBinnedSmoothingsmoothRawCopyNumbers.TotalCnKernelSmoothingsmoothRawCopyNumbers.TotalCnSmoothingSnpDatatestAllelicBalanceByBAFstestAllelicBalanceByBAFs.defaulttestEqualityC1C2ByChiSqtestEqualityC1C2ByMeantestEqualityC1orC2ByTtestEqualityTcnByMeantestEqualityTcnByTTotalCnBinnedSmoothingTotalCnKernelSmoothingTotalCnSmoothingTotalFracBSnpDatatransformC1C2transformC1C2.PairedPSCBStranslateC1C2translateC1C2.PairedPSCBSTumorBoostNormalizationXYCurveNormalization

Dependencies:aroma.corearoma.lightbase64encBiocManagercodetoolsdigestDNAcopyfuturefuture.applyglobalslistenvmatrixStatsparallellyPSCBSR.cacheR.devicesR.filesetsR.methodsS3R.ooR.rspR.utilsRColorBrewer