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:
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aroma.cn.pdf |aroma.cn.html✨
aroma.cn/json (API)
NEWS
# Install 'aroma.cn' in R: |
install.packages('aroma.cn', repos = c('https://henrikbengtsson.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/henrikbengtsson/aroma.cn/issues
Last updated 7 months agofrom:df71918f6f (on master). Checks:OK: 6 WARNING: 1. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 15 2024 |
R-4.5-win | OK | Aug 15 2024 |
R-4.5-linux | OK | Aug 15 2024 |
R-4.4-win | WARNING | Aug 15 2024 |
R-4.4-mac | OK | Aug 15 2024 |
R-4.3-win | OK | Aug 15 2024 |
R-4.3-mac | OK | Aug 15 2024 |
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
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Package aroma.cn | aroma.cn-package aroma.cn |
The AbstractCurveNormalization class | AbstractCurveNormalization |
Calls XX or XY from ChrX allele B fractions of a normal sample | callXXorXY callXXorXY.numeric |
The MultiSourceCopyNumberNormalization class | MultiSourceCopyNumberNormalization |
The PairedPscbsModel class | PairedPscbsModel |
The PrincipalCurveNormalization class | PrincipalCurveNormalization |
The TotalCnBinnedSmoothing class | TotalCnBinnedSmoothing |
The TotalCnKernelSmoothing class | TotalCnKernelSmoothing |
The abstract TotalCnSmoothing class | TotalCnSmoothing |
The TumorBoostNormalization class | TumorBoostNormalization |
The XYCurveNormalization class | XYCurveNormalization |