Non-documented objects

0th

Percentile

Non-documented objects

This page contains aliases for all "non-documented" objects that R CMD check detects in this package.

Almost all of them are generic functions that have specific document for the corresponding method coupled to a specific class. Other functions are re-defined by setMethodS3() to default methods. Neither of these two classes are non-documented in reality. The rest are deprecated methods.

Keywords
internal, documentation
Aliases
  • Non-documented objects
  • as.character.MultiSourceCopyNumberNormalization
  • extractTupleOfDataFiles
  • fitOne
  • getAllNames
  • getAsteriskTags.TotalCnSmoothing
  • getFitAromaUgpFile
  • getInputDataSets
  • getOutputDataSets
  • getOutputDataSets.MultiSourceCopyNumberNormalization
  • getOutputFiles.TotalCnSmoothing
  • getOutputPaths
  • getOutputPaths.MultiSourceCopyNumberNormalization
  • getParameters.MultiSourceCopyNumberNormalization
  • getParameters.TotalCnSmoothing
  • getParametersAsString.MultiSourceCopyNumberNormalization
  • getPath.TotalCnSmoothing
  • getRootPath.TotalCnSmoothing
  • getSmoothedDataSets
  • getSubsetToFit
  • getTargetPositions
  • getTargetPositions.TotalCnSmoothing
  • getTargetUgpFile
  • getTargetUgpFile.TotalCnSmoothing
  • makeSmoothSplinePredict
  • makeSmoothSplinePredict.numeric
  • nbrOfDataSets
  • nbrOfDataSets.MultiSourceCopyNumberNormalization
  • normalizeOne
  • normalizeOne.MultiSourceCopyNumberNormalization
  • normalizePrincipalCurve
  • pairs2
  • pairs2.principal.curve
  • process.TotalCnSmoothing
  • getAsteriskTags.TotalCnKernelSmoothing
  • getParameters.TotalCnKernelSmoothing
  • smoothRawCopyNumbers
  • smoothRawCopyNumbers.TotalCnKernelSmoothing
  • smoothRawCopyNumbers.TotalCnSmoothing
  • asCartesianSnpData
  • asCartesianSnpData.CartesianSnpData
  • asCartesianSnpData.PolarSnpData
  • asCartesianSnpData.TotalFracBSnpData
  • asPolarSnpData
  • asPolarSnpData.CartesianSnpData
  • asPolarSnpData.PolarSnpData
  • asPolarSnpData.TotalFracBSnpData
  • asTotalFracBSnpData
  • asTotalFracBSnpData.CartesianSnpData
  • asTotalFracBSnpData.PolarSnpData
  • asTotalFracBSnpData.TotalFracBSnpData
  • callGenotypes
  • callGenotypes.SnpData
  • callGenotypes.TotalFracBSnpData
  • CartesianSnpData
  • pairedBoost
  • pairedBoost.CartesianSnpData
  • pairedBoost.PolarSnpData
  • pairedBoost.TotalFracBSnpData
  • plot.CartesianSnpData
  • plot.PolarSnpData
  • plot.SnpData
  • plot.TotalFracBSnpData
  • PolarSnpData
  • SnpData
  • TotalFracBSnpData
  • as.character.TumorBoostNormalization
  • getDataSets
  • getDataSets.TumorBoostNormalization
  • getInputDataSet.TumorBoostNormalization
  • getNormalDataSet
  • getNormalDataSet.TumorBoostNormalization
  • getNormalGenotypeCallSet
  • getNormalGenotypeCallSet.TumorBoostNormalization
  • getOutputDataSet.TumorBoostNormalization
  • getOutputPath
  • getOutputPath.TumorBoostNormalization
  • getRootPath.TumorBoostNormalization
  • nbrOfFiles.TumorBoostNormalization
  • process.TumorBoostNormalization
  • getAsteriskTags.TumorBoostNormalization
  • getFullName.TumorBoostNormalization
  • getName.TumorBoostNormalization
  • getPath.TumorBoostNormalization
  • getTags.TumorBoostNormalization
  • setTags.TumorBoostNormalization
  • getAsteriskTags.MultiSourceCopyNumberNormalization
  • getTags.MultiSourceCopyNumberNormalization
  • getFlavor
  • getFlavor.TumorBoostNormalization
  • as.character.AbstractCurveNormalization
  • backtransformOne
  • backtransformOne.AbstractCurveNormalization
  • backtransformOne.PrincipalCurveNormalization
  • backtransformOne.XYCurveNormalization
  • fitOne.AbstractCurveNormalization
  • fitOne.PrincipalCurveNormalization
  • fitOne.XYCurveNormalization
  • getAsteriskTags.AbstractCurveNormalization
  • getDataSets.AbstractCurveNormalization
  • getFullName.AbstractCurveNormalization
  • getInputDataSet.AbstractCurveNormalization
  • getName.AbstractCurveNormalization
  • getOutputDataSet.AbstractCurveNormalization
  • getPairedDataSet.AbstractCurveNormalization
  • getPath.AbstractCurveNormalization
  • getRootPath.AbstractCurveNormalization
  • getSubsetToFit.AbstractCurveNormalization
  • getTags.AbstractCurveNormalization
  • getTargetDataSet.AbstractCurveNormalization
  • nbrOfFiles.AbstractCurveNormalization
  • process.AbstractCurveNormalization
  • setTags.AbstractCurveNormalization
  • getSubsetToFit.PrincipalCurveNormalization
  • getPairedDataSet
  • getTargetDataSet
  • callGenotypes.RawAlleleBFractions
  • getCalls
  • getCalls.RawGenotypeCalls
  • getColors
  • getColors.RawGenotypeCalls
  • isHeterozygous.RawGenotypeCalls
  • isHomozygous.RawGenotypeCalls
  • RawGenotypeCalls
  • normalizeTumorBoost.RawAlleleBFractions
  • plotSmoothedPairsOne
  • plotSmoothedPairsOne.MultiSourceCopyNumberNormalization
  • getBacktransforms
  • getBacktransforms.PrincipalCurve
  • getPrincipalCurveEstimator
  • getPrincipalCurveEstimator.MultiSourceCopyNumberNormalization
  • plotBacktransforms
  • plotBacktransforms.PrincipalCurve
  • getDataSet
  • getDataSet.NaiveFracBGenotyping
  • getGenotypeCallSet
  • getGenotypeCallSet.NaiveFracBGenotyping
  • NaiveFracBGenotyping
  • nbrOfLoci.NaiveFracBGenotyping
  • nbrOfSNPs
  • nbrOfSNPs.NaiveFracBGenotyping
  • process.NaiveFracBGenotyping
  • processOne
  • processOne.NaiveFracBGenotyping
  • segmentByPruneCBS
  • segmentByPruneCBS.RawGenomicSignals
  • normalizeBAFsByRegions
  • callAllelicBalanceByBAFs
  • callCopyNeutralRegions
  • getXScale.CopyNumberRegions
  • getYScale.CopyNumberRegions
  • plot.CopyNumberRegions
  • segmentByPruneCBSv1
  • segmentByPruneCBSv1.RawGenomicSignals
  • orthogonalizeC1C2
  • ABtoC1C2
  • bootstrap
  • bootstrap.PairedPSCBS
  • C1C2toAB
  • extractC1C2
  • extractC1C2.list
  • fitLoess2D
  • fitLoess2D.C1C2
  • fitLoessKD
  • fitLoessKD.data.frame
  • fitLoessKD.matrix
  • normalizeLoess2D
  • normalizeLoess2D.C1C2
  • normalizeLoessKD
  • normalizeLoessKD.data.frame
  • normalizeLoessKD.matrix
  • plot.C1C2
  • points.C1C2
  • resampleA
  • resampleA.PairedPSCBS
  • resampleB
  • resampleB.PairedPSCBS
  • resampleC
  • resampleC.PairedPSCBS
  • callPeaks
  • callPeaks.data.frame
  • estimateC2Bias
  • estimateC2Bias.PairedPSCBS
  • fitC1C2Densities
  • fitC1C2Densities.PairedPSCBS
  • fitC1C2Peaks
  • fitC1C2Peaks.PairedPSCBS
  • plotC1C2Grid
  • plotC1C2Grid.PairedPSCBS
  • translateC1C2
  • translateC1C2.PairedPSCBS
  • transformC1C2
  • transformC1C2.PairedPSCBS
  • PairedPSCBSFile
  • PairedPSCBSFileSet
  • byName.PairedPSCBSFileSet
  • byPath.PairedPSCBSFileSet
  • findAtomicAberrations.PairedPSCBS
  • findByName.PairedPSCBSFileSet
  • loadObject.PairedPSCBSFile
  • plotTracks
  • plotTracks.PruneCNA
  • pruneCNA
  • pruneCNA.PairedPSCBS
  • testEqualityC1C2ByChiSquare
  • testEqualityC1C2ByMean
  • testEqualityTcnByMean
  • testEqualityTcnByT
  • cat
  • getOption
  • drawC1C2Density
  • drawC1C2Density.PairedPSCBS
  • getAsteriskTags.TotalCnBinnedSmoothing
  • getParameters.TotalCnBinnedSmoothing
  • smoothRawCopyNumbers.TotalCnBinnedSmoothing
  • findAtomicAberrations.CBS
  • pruneCNA.AbstractCBS
  • [.PruneCNA
  • extractGenerations
  • extractGenerations.PruneCNA
  • nbrOfGenerations
  • nbrOfGenerations.PruneCNA
  • testEqualityC1C2ByChiSq
  • testEqualityC1orC2ByT
  • as.character.PairedPscbsModel
  • fit.PairedPscbsModel
  • getAsteriskTags.PairedPscbsModel
  • getChipType.PairedPscbsModel
  • getChromosomes.PairedPscbsModel
  • getDataSets.PairedPscbsModel
  • getFitFunction.PairedPscbsModel
  • getFullName.PairedPscbsModel
  • getName.PairedPscbsModel
  • getNormalDataSet.PairedPscbsModel
  • getOptionalArguments.PairedPscbsModel
  • getParameters.PairedPscbsModel
  • getParametersAsString.PairedPscbsModel
  • getPath.PairedPscbsModel
  • getRandomSeed.PairedPscbsModel
  • getRootPath.PairedPscbsModel
  • getTags.PairedPscbsModel
  • getTumorDataSet
  • getTumorDataSet.PairedPscbsModel
  • indexOf.PairedPscbsModel
  • nbrOfFiles.PairedPscbsModel
  • setRandomSeed.PairedPscbsModel
  • setTags.PairedPscbsModel
  • calculatePairedPSCNByGenotype
  • calculatePairedPSCNByGenotype.data.frame
  • calculatePairedPSCNByGenotype.numeric
  • calculateTumorPSCNByGenotypeUsingCTCN
  • calculateTumorPSCNByGenotypeUsingCTCN.numeric
  • PairedPscbsCaller
  • getAsteriskTags.PairedPscbsCaller
  • getParameters.PairedPscbsCaller
  • getPath.PairedPscbsCaller
  • getPlatform.PairedPscbsCaller
  • getRootPath.PairedPscbsCaller
  • process.PairedPscbsCaller
  • getOutputDataSet.PairedPscbsModel
  • loadFit.PairedPSCBSFile
  • getChipType.PairedPSCBSFileSet
  • getDefaultFullName.PairedPSCBSFileSet
  • getPlatform.PairedPSCBSFileSet
  • getOptionalArguments.PairedPscbsCaller
  • backgroundCorrect
  • backgroundCorrect.PairedPSCBS
  • getOutputDataSet0.TotalCnSmoothing
  • getOutputFileClass
  • getOutputFileClass.TotalCnSmoothing
  • getOutputFileExtension
  • getOutputFileExtension.TotalCnSmoothing
  • getOutputFileSetClass
  • getOutputFileSetClass.TotalCnSmoothing
  • doSegmentByPairedPSCBS
  • doSegmentByPairedPSCBS.AromaUnitPscnBinarySet
  • findLargeGaps.AromaUgpFile
  • findLargeGaps.AromaUnitPscnBinarySet
Documentation reproduced from package aroma.cn, version 1.6.1, License: LGPL (>= 2.1)

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