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
  • #
  • DEFUNCT
  • /
  • DEPRECATED
  • nbrOfArrays
  • MISC.
  • applyTo
  • applyTo.SampleAnnotationFile
  • [.AromaTabularBinaryFile
  • [[.AromaTabularBinaryFile
  • [<-.AromaTabularBinaryFile
  • addBy
  • addBy.RawGenomicSignals
  • addIncludes
  • addIncludes.Explorer
  • addIndexFile
  • addIndexFile.ChromosomeExplorer
  • addIndexFile.Explorer
  • addLocusFields
  • addLocusFields.RawGenomicSignals
  • allocate
  • allocate.AromaCellPositionFile
  • allocate.AromaCellSequenceFile
  • allocate.AromaMicroarrayTabularBinaryFile
  • allocate.AromaUflFile
  • allocate.AromaUgpFile
  • allocate.AromaUnitCallFile
  • allocate.AromaUnitChromosomeTabularBinaryFile
  • allocate.AromaUnitGenotypeCallFile
  • allocate.AromaUnitSignalBinaryFile
  • allocate.AromaUnitTypesFile
  • allocateFromUnitAnnotationDataFile
  • allocateFromUnitAnnotationDataFile.AromaUnitSignalBinaryFile
  • allocateFromUnitAnnotationDataFile.AromaUnitTabularBinaryFile
  • allocateFromUnitNamesFile
  • allocateFromUnitNamesFile.AromaUnitSignalBinaryFile
  • allocateFromUnitNamesFile.AromaUnitTabularBinaryFile
  • append.RawGenomicSignals
  • applyBinaryOperator
  • applyBinaryOperator.RawGenomicSignals
  • applyRegions
  • applyRegions.CopyNumberOutliers
  • applyRows
  • applyRows.CopyNumberRegions
  • AromaCellSequenceFile
  • AromaCore
  • AromaPackage
  • aromaSettings
  • AromaSettings
  • AromaUflFile
  • AromaUgpFile
  • AromaUnitChromosomeTabularBinaryFile
  • AromaUnitTotalCnBinaryFileList
  • AromaUnitTotalCnBinarySetTuple
  • as.AromaMicroarrayDataSetList
  • as.AromaMicroarrayDataSetList.AromaMicroarrayDataSet
  • as.AromaMicroarrayDataSetTuple
  • as.AromaMicroarrayDataSetTuple.AromaMicroarrayDataSet
  • as.AromaMicroarrayDataSetTuple.AromaMicroarrayDataSetTuple
  • as.AromaUnitTotalCnBinarySetTuple
  • as.AromaUnitTotalCnBinarySetTuple.AromaUnitTotalCnBinarySet
  • as.AromaUnitTotalCnBinarySetTuple.AromaUnitTotalCnBinarySetTuple
  • as.character.AromaMicroarrayDataSetTuple
  • as.character.AromaMicroarrayTabularBinaryFile
  • as.character.AromaTabularBinaryFile
  • as.character.AromaTransform
  • as.character.AromaUnitSignalBinaryFile
  • as.character.ChromosomalModel
  • as.character.ChromosomeExplorer
  • as.character.CopyNumberChromosomalModel
  • as.character.CopyNumberOutliers
  • as.character.CopyNumberRegions
  • as.character.Explorer
  • as.character.RawGenomicSignals
  • as.character.TextUnitNamesFile
  • as.CopyNumberDataFile
  • as.CopyNumberDataFile.CopyNumberDataFile
  • as.CopyNumberDataSet
  • as.CopyNumberDataSet.CopyNumberDataSet
  • as.CopyNumberDataSetTuple
  • as.CopyNumberDataSetTuple.AromaUnitTotalCnBinarySet
  • as.CopyNumberDataSetTuple.CopyNumberDataSetTuple
  • as.CopyNumberDataSetTuple.list
  • as.data.frame.CopyNumberOutliers
  • as.data.frame.CopyNumberRegions
  • as.data.frame.RawCopyNumbers
  • as.data.frame.RawGenomicSignals
  • as.data.frame.SegmentedGenomicSignalsInterface
  • as.GrayscaleImage
  • as.TrueColorImage
  • as.TrueColorImage.Image
  • as.TrueColorImage.matrix
  • asMatrixOfFiles
  • asMatrixOfFiles.AromaMicroarrayDataSetTuple
  • asThis
  • asThis.BasicObject
  • asThis.Object
  • backtransformGenotypeCone
  • backtransformGenotypeCone.matrix
  • backtransformMultiDimensionalCone
  • backtransformMultiDimensionalCone.matrix
  • barSequence
  • barSequence.ProbePositionEffects
  • binnedSmoothing.RawGenomicSignals
  • binnedSmoothingByState
  • binnedSmoothingByState.SegmentedGenomicSignalsInterface
  • binnedSums
  • binnedSums.RawSequenceReads
  • binScatter
  • binScatter.matrix
  • byChipType
  • byChipType.AromaCellTabularBinaryFile
  • byChipType.AromaMicroarrayTabularBinaryFile
  • byChipType.AromaUnitTabularBinaryFile
  • byChipType.UnitAnnotationDataFile
  • byName.AromaPlatform
  • byName.AromaUnitFracBCnBinarySet
  • byName.AromaUnitGenotypeCallSet
  • byName.AromaUnitSignalBinarySet
  • byName.AromaUnitTotalCnBinarySet
  • byPath.AromaMicroarrayDataSetTuple
  • byPath.AromaUnitCallSet
  • byPath.AromaUnitGenotypeCallSet
  • calcMargins
  • calcMargins.matrix
  • calculateAverageColumnAcrossFiles
  • calculateAverageColumnAcrossFiles.GenericTabularFileSet
  • calculateChromosomeStatistics
  • calculateChromosomeStatistics.CopyNumberChromosomalModel
  • calculateRatios
  • calculateRatios.CopyNumberChromosomalModel
  • cnRange
  • cnRange.RawCopyNumbers
  • colGaussianSmoothing
  • colGaussianSmoothing.matrix
  • colMeans
  • colMeans.AromaTabularBinaryFile
  • colMeans.default
  • colorize
  • colorize.Image
  • colStats
  • colStats.AromaTabularBinaryFile
  • colSums
  • colSums.AromaTabularBinaryFile
  • colSums.default
  • convertTable
  • convertTable.default
  • CopyNumberDataFile
  • CopyNumberDataSet
  • CopyNumberDataSetTuple
  • CopyNumberOutliers
  • CopyNumberRegions
  • countBases
  • countBases.AromaCellSequenceFile
  • countBasesInternal
  • countBasesInternal.AromaCellSequenceFile
  • dimnames<-.AromaTabularBinaryFile
  • display
  • display.ChromosomeExplorer
  • display.Image
  • divideBy
  • divideBy.RawGenomicSignals
  • drawCnRegions
  • drawCnRegions.DNAcopy
  • drawCnRegions.HaarSeg
  • drawCnRegions.profileCGH
  • drawCytoband
  • drawCytoband.ChromosomalModel
  • drawCytoband.profileCGH
  • drawCytoband2
  • drawCytoband2.default
  • drawExtraAnnotations
  • drawExtraAnnotations.default
  • drawExtraAnnotations.profileCGH
  • drawLevels
  • drawLevels.CopyNumberOutliers
  • drawLevels.CopyNumberRegions
  • estimateSds
  • estimateStandardDeviation
  • exportFracBDiffSet
  • exportFracBDiffSet.AromaUnitFracBCnBinarySet
  • exportTotalCnRatioSet
  • exportTotalCnRatioSet.AromaUnitTotalCnBinarySet
  • extractByChromosome
  • extractByChromosome.AromaUnitChromosomeTabularBinaryFile
  • extractCallArray
  • extractCallArray.AromaUnitCallFile
  • extractCallArray.AromaUnitCallSet
  • extractCalls
  • extractCalls.AromaUnitCallFile
  • extractCalls.AromaUnitCallSet
  • extractCNRs
  • extractCNRs.default
  • extractCopyNumberOutliers
  • extractCopyNumberOutliers.DNAcopy
  • extractCopyNumberOutliers.profileCGH
  • extractCopyNumberRegions
  • extractCopyNumberRegions.default
  • extractCopyNumberRegions.DNAcopy
  • extractCopyNumberRegions.HaarSeg
  • extractCopyNumberRegions.profileCGH
  • extractDataForSegmentation
  • extractDataForSegmentation.RawGenomicSignals
  • extractGenotypeMatrix
  • extractGenotypeMatrix.AromaUnitCallSet
  • extractGenotypeMatrix.AromaUnitGenotypeCallFile
  • extractGenotypes
  • extractGenotypes.AromaUnitGenotypeCallFile
  • extractGenotypes.AromaUnitGenotypeCallSet
  • extractIGV
  • extractIGV.CopyNumberRegions
  • extractMatrix.AromaUnitCallFile
  • extractMatrix.AromaUnitSignalBinaryFile
  • extractMergedRawCopyNumbers
  • extractMergedRawCopyNumbers.AromaUnitTotalCnBinaryFileList
  • extractOld
  • extractOld.AromaMicroarrayDataSetTuple
  • extractRawAlleleBFractions
  • extractRawAlleleBFractions.AromaUnitFracBCnBinaryFile
  • extractRawAlleleBFractions.default
  • extractRawCNs
  • extractRawCNs.default
  • extractRawCopyNumbers
  • extractRawCopyNumbers.AromaUnitTotalCnBinaryFile
  • extractRawCopyNumbers.AromaUnitTotalCnBinaryFileList
  • extractRawCopyNumbers.default
  • extractRawCopyNumbers.DNAcopy
  • extractRawCopyNumbers.HaarSeg
  • extractRawCopyNumbers.profileCGH
  • extractRawCopyNumbers.RawCopyNumbers
  • extractRawCopyNumbers.RawSequenceReads
  • extractRawGenomicSignals
  • extractRawGenomicSignals.AromaUnitSignalBinaryFile
  • extractRawGenomicSignals.AromaUnitTotalCnBinaryFileList
  • extractRawGenomicSignals.default
  • extractRawMirroredAlleleBFractions
  • extractRawMirroredAlleleBFractions.default
  • extractRawMirroredAlleleBFractions.RawAlleleBFractions
  • extractRegion
  • extractRegion.RawGenomicSignals
  • extractSubset
  • extractSubset.RawGenomicSignals
  • extractSubsetByState
  • extractSubsetByState.SegmentedGenomicSignalsInterface
  • findByChipType
  • findByChipType.AromaMicroarrayTabularBinaryFile
  • findByChipType.TextUnitNamesFile
  • findByName.AromaUnitCallSet
  • findByName.AromaUnitSignalBinarySet
  • findPngDevice
  • findPngDevice.default
  • findSAFs
  • findSAFs.SampleAnnotationSet
  • findUnitNamesFile
  • findUnitNamesFile.AromaPlatform
  • findUnitsTodo
  • findUnitsTodo.AromaUnitCallFile
  • findUnitsTodo.AromaUnitCallSet
  • findUnitTypesFile
  • findUnitTypesFile.AromaPlatform
  • fit
  • fit.ChromosomalModel
  • fit2d
  • fit2d.matrix
  • fitGenotypeCone
  • fitGenotypeConeByExpectile
  • fitGenotypeConeByExpectile.matrix
  • fitGenotypeConeBySfit
  • fitMultiDimensionalCone
  • fitProbePositionEffects
  • fitProbePositionEffects.numeric
  • fitSplineBlockPolish
  • fitSplineBlockPolish.matrix
  • fitWHLAPLM
  • fitWHLAPLM.matrix
  • fitWHRCModel
  • fitWHRCModel.matrix
  • fitWLAPLM
  • fitWLAPLM.matrix
  • fitWRCModel
  • fitWRCModel.matrix
  • fitWRMA
  • fitWRMA.matrix
  • fixSearchPath
  • fixSearchPath.AromaCore
  • fixSearchPath.AromaPackage
  • fixSearchPathInternal
  • fixSearchPathInternal.AromaPackage
  • fromFile.AromaUnitSignalBinaryFile
  • fromPath
  • fromPath.SampleAnnotationFile
  • fromPath.SampleAnnotationSet
  • gaussianSmoothing
  • gaussianSmoothing.matrix
  • gaussianSmoothing.numeric
  • gaussianSmoothing.RawGenomicSignals
  • gaussKernel
  • getAlias.ChromosomalModel
  • getAM
  • getAM.AromaUnitTotalCnBinaryFile
  • getAromaPlatform
  • getAromaUflFile
  • getAromaUflFile.UnitAnnotationDataFile
  • getAromaUgpFile
  • getAromaUgpFile.AromaPlatform
  • getAromaUgpFile.AromaUnitSignalBinaryFile
  • getAromaUgpFile.AromaUnitSignalBinarySet
  • getAromaUgpFile.UnitAnnotationDataFile
  • getArrays
  • getArrays.AromaMicroarrayDataSetTuple
  • getArrays.ChromosomalModel
  • getArrays.Explorer
  • getArraysOfInput
  • getArraysOfInput.ChromosomeExplorer
  • getArraysOfInput.Explorer
  • getArrayTuple
  • getArrayTuple.AromaMicroarrayDataSetTuple
  • getAsteriskTags.AromaMicroarrayDataSetTuple
  • getAsteriskTags.AromaTransform
  • getAsteriskTags.ChromosomalModel
  • getAsteriskTags.CopyNumberSegmentationModel
  • getAsteriskTags.Explorer
  • getAsteriskTags.HaarSegModel
  • getAsteriskTags.RawCopyNumberModel
  • getAttributeXY
  • getAttributeXY.AromaMicroarrayDataFile
  • getAverageFile
  • getAverageFile.AromaMicroarrayDataSet
  • getAverageFile.AromaUnitTotalCnBinarySet
  • getBytesPerColumn
  • getBytesPerColumn.AromaTabularBinaryFile
  • getChipEffectFiles
  • getChipEffectFiles.ChromosomalModel
  • getChipType
  • getChipType.AromaMicroarrayDataFile
  • getChipType.AromaMicroarrayDataSet
  • getChipType.AromaMicroarrayTabularBinaryFile
  • getChipType.AromaUnitSignalBinaryFile
  • getChipType.AromaUnitSignalBinarySet
  • getChipType.AromaUnitTypesFile
  • getChipType.TextUnitNamesFile
  • getChipType.UnitAnnotationDataFile
  • getChipTypes
  • getChipTypes.AromaMicroarrayDataSetTuple
  • getChipTypes.ChromosomalModel
  • getChromosome
  • getChromosome.Arguments
  • getChromosome.RawGenomicSignals
  • getChromosomes
  • getChromosomes.Arguments
  • getChromosomes.AromaUnitChromosomeTabularBinaryFile
  • getCn
  • getCn.RawCopyNumbers
  • getCNs
  • getCNs.RawCopyNumbers
  • getColClasses
  • getColClasses.AromaTabularBinaryFile
  • getColumnNames.AromaCellPositionFile
  • getColumnNames.AromaCellSequenceFile
  • getColumnNames.AromaTabularBinaryFile
  • getColumnNames.AromaUflFile
  • getColumnNames.AromaUgpFile
  • getColumnNames.AromaUnitChromosomeTabularBinaryFile
  • getCommonListElements
  • getDataFileMatrix
  • getDataFileMatrix.CopyNumberChromosomalModel
  • getDeviceResolution
  • getDeviceResolution.default
  • getEffects
  • getEffects.ProbePositionEffects
  • getExpectedOutputFiles
  • getExpectedOutputFiles.AromaTransform
  • getExpectedOutputFullnames
  • getExpectedOutputFullnames.AromaTransform
  • getExtensionPattern.AromaCellPositionFile
  • getExtensionPattern.AromaCellSequenceFile
  • getExtensionPattern.AromaUflFile
  • getExtensionPattern.AromaUgpFile
  • getExtensionPattern.AromaUnitSignalBinaryFile
  • getExtensionPattern.SampleAnnotationFile
  • getExtensionPattern.TextUnitNamesFile
  • getFilenameExtension.AromaCellPositionFile
  • getFilenameExtension.AromaCellSequenceFile
  • getFilenameExtension.AromaMicroarrayTabularBinaryFile
  • getFilenameExtension.AromaUflFile
  • getFilenameExtension.AromaUgpFile
  • getFilenameExtension.AromaUnitChromosomeTabularBinaryFile
  • getFilenameExtension.AromaUnitSignalBinaryFile
  • getFilenameExtension.TextUnitNamesFile
  • getFitFunction
  • getFitFunction.CbsModel
  • getFitFunction.CopyNumberSegmentationModel
  • getFitFunction.GladModel
  • getFitFunction.HaarSegModel
  • getFullName.ChromosomalModel
  • getFullName.Explorer
  • getFullNames.AromaMicroarrayDataSetTuple
  • getFullNames.ChromosomalModel
  • getFullNames.ChromosomeExplorer
  • getFullNames.CopyNumberSegmentationModel
  • getGenome
  • getGenome.ChromosomalModel
  • getGenomeData
  • getGenomeData.ChromosomalModel
  • getGenomeFile
  • getGenomeFile.ChromosomalModel
  • getGenomeVersion
  • getGenomeVersion.AromaUnitChromosomeTabularBinaryFile
  • getHeaderParameters
  • getHeaderParameters.TextUnitNamesFile
  • getImage
  • getImage.matrix
  • getIncludePath
  • getIncludePath.Explorer
  • getInputDataSet
  • getListOfAromaUgpFiles
  • getListOfAromaUgpFiles.ChromosomalModel
  • getListOfChipEffectSets
  • getListOfChipEffectSets.ChromosomalModel
  • getListOfUnitNamesFiles
  • getListOfUnitNamesFiles.AromaUnitTotalCnBinarySetTuple
  • getListOfUnitNamesFiles.ChromosomalModel
  • getListOfUnitTypesFiles
  • getListOfUnitTypesFiles.ChromosomalModel
  • getLociFields
  • getLociFields.RawGenomicSignals
  • getLocusFields
  • getLocusFields.RawGenomicSignals
  • getLog2Ratios
  • getLog2Ratios.CopyNumberSegmentationModel
  • getMainPath
  • getMainPath.Explorer
  • getMaxLengthRepeats
  • getMaxLengthRepeats.AromaCellSequenceFile
  • getModel
  • getName.AromaPlatform
  • getName.ChromosomalModel
  • getName.RawGenomicSignals
  • getNameOfInput
  • getNameOfInput.ChromosomeExplorer
  • getNameOfInput.Explorer
  • getNames.ChromosomeExplorer
  • getNames.CopyNumberChromosomalModel
  • getNumberOfFilesAveraged
  • getNumberOfFilesAveraged.CopyNumberDataFile
  • getOutputDataSet
  • getOutputDataSet0
  • getOutputDataSet0.AromaTransform
  • getOutputFiles
  • getOutputFiles.AromaTransform
  • getPairedNames
  • getPairedNames.CopyNumberChromosomalModel
  • getParallelSafe
  • getParallelSafe.Explorer
  • getParametersAsString
  • getParentPath
  • getParentPath.ChromosomalModel
  • getPath.ChromosomalModel
  • getPath.ChromosomeExplorer
  • getPatterns
  • getPatterns.SampleAnnotationFile
  • getPhysicalPositions
  • getPhysicalPositions.RawCopyNumbers
  • getPlatform
  • getPlatform.AromaMicroarrayDataFile
  • getPlatform.AromaMicroarrayDataSet
  • getPlatform.AromaMicroarrayTabularBinaryFile
  • getPlatform.AromaUnitSignalBinaryFile
  • getPlatform.AromaUnitSignalBinarySet
  • getPlatform.AromaUnitTypesFile
  • getPlatform.TextUnitNamesFile
  • getPlatform.UnitAnnotationDataFile
  • getPloidy
  • getPloidy.AromaMicroarrayDataFile
  • getPositions
  • getPositions.AromaUgpFile
  • getPositions.RawGenomicSignals
  • getProbeLength
  • getProbeLength.AromaCellSequenceFile
  • getProbePositionEffectDesignMatrix
  • getProbePositionEffectDesignMatrix.character
  • getProbePositionEffectDesignMatrix.raw
  • getRam
  • getRam.AromaSettings
  • getRawCnData
  • getRawCnData.CopyNumberChromosomalModel
  • getReferenceSetTuple
  • getReferenceSetTuple.CopyNumberChromosomalModel
  • getRefSetTuple
  • getRefSetTuple.CopyNumberChromosomalModel
  • getRegions
  • getRegions.CopyNumberSegmentationModel
  • getReportPath
  • getReportPath.ChromosomalModel
  • getReportPathPattern
  • getReportPathPattern.Explorer
  • getRootPath
  • getRootPath.ChromosomalModel
  • getSampleLabels
  • getSampleLabels.ChromosomeExplorer
  • getSampleLayerName
  • getSampleLayerName.Explorer
  • getSampleLayerPrefix
  • getSampleLayerPrefix.Explorer
  • getSets.AromaMicroarrayDataSetTuple
  • getSets.ChromosomalModel
  • getSetTag
  • getSetTag.ChromosomalModel
  • getSetTag.RawCopyNumberModel
  • getSetTuple
  • getSetTuple.ChromosomalModel
  • getSigma
  • getSigma.RawGenomicSignals
  • getSignals
  • getSignals.RawGenomicSignals
  • getSnpNucleotides
  • getSnpNucleotides.AromaCellSequenceFile
  • getSnpPositions
  • getSnpPositions.AromaCellSequenceFile
  • getSnpShifts
  • getSnpShifts.AromaCellSequenceFile
  • getStateColorMap
  • getStateColorMap.SegmentedGenomicSignalsInterface
  • getStateColors
  • getStateColors.SegmentedGenomicSignalsInterface
  • getStates
  • getStates.SegmentedGenomicSignalsInterface
  • getSubname
  • getSubname.Explorer
  • getTableOfArrays
  • getTableOfArrays.AromaMicroarrayDataSetTuple
  • getTableOfArrays.ChromosomalModel
  • getTags.AromaMicroarrayDataSetTuple
  • getTags.ChromosomalModel
  • getTags.CopyNumberSegmentationModel
  • getTagsOfInput
  • getTagsOfInput.ChromosomeExplorer
  • getTagsOfInput.Explorer
  • getTemplatePath
  • getTemplatePath.Explorer
  • getUniqueStates
  • getUniqueStates.SegmentedGenomicSignalsInterface
  • getUnitAnnotationDataFile
  • getUnitNames.TextUnitNamesFile
  • getUnitNames.UnitNamesFile
  • getUnitNamesFile
  • getUnitNamesFile.AromaPlatform
  • getUnitNamesFile.AromaUnitTotalCnBinarySet
  • getUnitsAt
  • getUnitsAt.AromaUgpFile
  • getUnitsOnChromosome
  • getUnitsOnChromosome.AromaUgpFile
  • getUnitsOnChromosome.AromaUnitChromosomeTabularBinaryFile
  • getUnitsOnChromosomes
  • getUnitsOnChromosomes.AromaUnitChromosomeTabularBinaryFile
  • getUnitTypes
  • getUnitTypes.AromaUnitTypesFile
  • getUnitTypes.UnitTypesFile
  • getUnitTypesFile
  • getUnitTypesFile.AromaPlatform
  • getVerbose.AromaSettings
  • getWeights
  • getWeights.RawGenomicSignals
  • getXAM
  • getXAM.AromaMicroarrayDataFile
  • getXAM.AromaUnitTotalCnBinaryFile
  • getXScale
  • getXScale.RawGenomicSignals
  • getXY
  • getXY.RawGenomicSignals
  • getYScale
  • getYScale.RawGenomicSignals
  • getZooms
  • getZooms.ChromosomeExplorer
  • groupBySnpNucleotides
  • groupBySnpNucleotides.AromaCellSequenceFile
  • hasAlleleBFractions
  • hasAlleleBFractions.AromaUnitTotalCnBinaryFile
  • hasAlleleBFractions.CopyNumberDataFile
  • hasAlleleBFractions.CopyNumberDataSet
  • hasAlleleBFractions.CopyNumberDataSetTuple
  • hasAttributeXY
  • hasAttributeXY.AromaMicroarrayDataFile
  • hasStrandiness
  • hasStrandiness.AromaUnitTotalCnBinaryFile
  • hasStrandiness.CopyNumberDataFile
  • hasStrandiness.CopyNumberDataSet
  • hasStrandiness.CopyNumberDataSetTuple
  • hasWeights
  • hasWeights.RawGenomicSignals
  • importFrom
  • importFrom.AromaTabularBinaryFile
  • importFromGenericTabularFile
  • importFromGenericTabularFile.AromaUflFile
  • importFromGenericTabularFile.AromaUgpFile
  • importFromTable
  • importFromTable.FileMatrix
  • importFromUnitTypesFile
  • importFromUnitTypesFile.AromaUnitTypesFile
  • indexOf.AromaMicroarrayDataSetTuple
  • indexOf.ChromosomalModel
  • indexOf.ChromosomeExplorer
  • indexOfColumn
  • indexOfColumn.AromaUnitChromosomeTabularBinaryFile
  • indexOfUnits
  • indexOfUnits.AromaUnitTabularBinaryFile
  • interleave
  • interleave.Image
  • isAverageFile
  • isAverageFile.AromaMicroarrayDataFile
  • isAverageFile.AromaUnitSignalBinaryFile
  • isHeterozygote
  • isHeterozygote.AromaUnitGenotypeCallFile
  • isHeterozygous
  • isHeterozygous.AromaUnitGenotypeCallFile
  • isHomozygote
  • isHomozygote.AromaUnitGenotypeCallFile
  • isHomozygous
  • isHomozygous.AromaUnitGenotypeCallFile
  • isMissing
  • isMissing.AromaCellPositionFile
  • isMissing.AromaCellSequenceFile
  • isPaired
  • isPaired.CopyNumberChromosomalModel
  • kernelSmoothing.RawGenomicSignals
  • kernelSmoothingByState
  • kernelSmoothingByState.SegmentedGenomicSignalsInterface
  • colApply
  • colApply.AromaTabularBinaryFile
  • lapplyInChunks
  • lapplyInChunks.numeric
  • library
  • lines.CopyNumberOutliers
  • lines.CopyNumberRegions
  • lines.RawGenomicSignals
  • listToXml
  • listToXml.list
  • locallyUnique
  • locallyUnique.default
  • log2abs
  • log2center
  • log2neg
  • log2pos
  • matchPatterns
  • matchPatterns.SampleAnnotationFile
  • matrixBlockPolish
  • mergeBoxplotStats
  • multiplyBy
  • multiplyBy.RawGenomicSignals
  • nbrOfCells
  • nbrOfCells.AromaCellTabularBinaryFile
  • nbrOfChipTypes
  • nbrOfColumns.AromaTabularBinaryFile
  • nbrOfEnzymes
  • nbrOfEnzymes.AromaUflFile
  • nbrOfLoci
  • nbrOfLoci.RawGenomicSignals
  • nbrOfReads
  • nbrOfReads.RawSequenceReads
  • nbrOfRegions
  • nbrOfRegions.CopyNumberOutliers
  • nbrOfRegions.CopyNumberRegions
  • nbrOfRows.AromaTabularBinaryFile
  • nbrOfUnits
  • nbrOfUnits.AromaUnitSignalBinaryFile
  • nbrOfUnits.AromaUnitTabularBinaryFile
  • nbrOfUnits.TextUnitNamesFile
  • nbrOfUnits.UnitAnnotationDataFile
  • nbrOfUnits.UnitNamesFile
  • nbrOfUnits.UnitTypesFile
  • newPlot
  • newPlot.CopyNumberChromosomalModel
  • norm2d
  • norm2d.matrix
  • normalizeGenotypeCone
  • normalizeGenotypeCone.matrix
  • onFitAddGenotypeCalls
  • onFitAddGenotypeCalls.default
  • onFitAddGenotypeCalls.GladModel
  • plot.BinnedScatter
  • plot.CopyNumberSegmentationModel
  • plot.ProbePositionEffects
  • plot.RawAlleleBFractions
  • plot.RawCopyNumbers
  • plot.RawGenomicSignals
  • plot.RawMirroredAlleleBFractions
  • plot.RawSequenceReads
  • plot.SegmentedGenomicSignalsInterface
  • plotAxesLayers
  • plotAxesLayers.CopyNumberChromosomalModel
  • plotChromosomesLayers
  • plotChromosomesLayers.CopyNumberChromosomalModel
  • plotCopyNumberRegionLayers
  • plotCopyNumberRegionLayers.CopyNumberSegmentationModel
  • plotCytobandLayers
  • plotCytobandLayers.CopyNumberChromosomalModel
  • plotFitLayers
  • plotFitLayers.CopyNumberChromosomalModel
  • plotGridHorizontalLayers
  • plotGridHorizontalLayers.CopyNumberChromosomalModel
  • plotProfile2
  • plotProfile2.profileCGH
  • plotRawCNs
  • plotRawCNs.profileCGH
  • plotRawCopyNumbers
  • plotRawCopyNumbers.CopyNumberChromosomalModel
  • plotSampleLayers
  • plotSampleLayers.CopyNumberChromosomalModel
  • points.BinnedScatter
  • points.RawGenomicSignals
  • points.SegmentedGenomicSignalsInterface
  • pointsRawCNs
  • pointsRawCNs.default
  • pointsRawCNs.profileCGH
  • pointsSequence
  • pointsSequence.ProbePositionEffects
  • predict.ProbePositionEffects
  • readColumns.AromaTabularBinaryFile
  • readDataFrame.AromaTabularBinaryFile
  • readDataFrame.AromaUflFile
  • readDataFrame.AromaUnitChromosomeTabularBinaryFile
  • readDataFrame.AromaUnitSignalBinaryFile
  • readDataFrame.SampleAnnotationFile
  • readFooter
  • readHeader
  • readHeader.AromaTabularBinaryFile
  • readNeighborSequenceMatrix
  • readNeighborSequenceMatrix.AromaCellSequenceFile
  • readPairSequenceMatrix
  • readPairSequenceMatrix.AromaCellSequenceFile
  • readPositions
  • readPositions.AromaCellPositionFile
  • readRawFooter
  • readRawFooter.AromaTabularBinaryFile
  • readSequenceMatrix
  • readSequenceMatrix.AromaCellSequenceFile
  • readSequences
  • readSequences.AromaCellSequenceFile
  • readTargetStrands
  • readTargetStrands.AromaCellSequenceFile
  • remap
  • remap.default
  • reorder.BinnedScatter
  • require
  • rescale
  • rescale.Image
  • rgbTransform
  • rgbTransform.Image
  • SampleAnnotationFile
  • SampleAnnotationSet
  • segmentByCBS
  • segmentByGLAD
  • segmentByHaarSeg
  • setAlias.ChromosomalModel
  • setArrays
  • setAttributesBy.AromaMicroarrayDataSet
  • setAttributesBySampleAnnotationFile
  • setAttributesBySampleAnnotationFile.AromaMicroarrayDataSet
  • setAttributesBySampleAnnotationSet
  • setAttributesBySampleAnnotationSet.AromaMicroarrayDataSet
  • setAttributesByTags.AromaMicroarrayDataFile
  • setAttributesByTags.AromaTabularBinaryFile
  • setAttributeXY
  • setAttributeXY.AromaMicroarrayDataFile
  • setCytoband
  • setCytoband.ChromosomeExplorer
  • setGenome
  • setGenome.ChromosomalModel
  • setLocusFields
  • setLocusFields.RawGenomicSignals
  • setName.RawGenomicSignals
  • setParallelSafe
  • setParallelSafe.Explorer
  • setRam
  • setRam.AromaSettings
  • setReportPathPattern
  • setReportPathPattern.Explorer
  • setSigma
  • setSigma.RawGenomicSignals
  • setStateColorMap
  • setStateColorMap.SegmentedGenomicSignalsInterface
  • setStates
  • setStates.SegmentedGenomicSignalsInterface
  • setSubname
  • setSubname.Explorer
  • setTags.AromaTransform
  • setup
  • setup.ChromosomeExplorer
  • setup.Explorer
  • setVerbose
  • setVerbose.AromaSettings
  • setWeights
  • setWeights.RawGenomicSignals
  • setXScale
  • setXScale.RawGenomicSignals
  • setYScale
  • setYScale.RawGenomicSignals
  • setZooms
  • setZooms.ChromosomeExplorer
  • shakyText
  • shakyText.default
  • signalRange
  • signalRange.RawGenomicSignals
  • smoothWRMA
  • smoothWRMA.matrix
  • smoothWSA
  • smoothWSA.matrix
  • sort.RawGenomicSignals
  • splitByReportPathPattern
  • splitByReportPathPattern.Explorer
  • splitInChunks
  • splitInChunks.numeric
  • sqrtabs
  • sqrtcenter
  • sqrtneg
  • sqrtpos
  • sqrtsign
  • stextChipType
  • stextChipType.character
  • stextLabel
  • stextLabel.AromaMicroarrayDataFile
  • stextLabels
  • stextLabels.AromaMicroarrayDataFile
  • stextSize
  • stextSize.AromaMicroarrayDataFile
  • stringTree
  • stringTree.character
  • subsample
  • subsample.BinnedScatter
  • subset.AromaTabularBinaryFile
  • subset.BinnedScatter
  • subtractBy
  • subtractBy.RawGenomicSignals
  • summary.AromaTabularBinaryFile
  • summary.RawGenomicSignals
  • summaryOfUnits
  • summaryOfUnits.AromaUflFile
  • text.ProbePositionEffects
  • textSequence
  • textSequence.ProbePositionEffects
  • TextUnitNamesFile
  • updateData
  • updateData.AromaTabularBinaryFile
  • updateDataColumn
  • updateDataColumn.AromaTabularBinaryFile
  • updateGenotypes
  • updateGenotypes.AromaUnitGenotypeCallFile
  • updatePositions
  • updatePositions.AromaCellPositionFile
  • updateSequenceMatrix
  • updateSequenceMatrix.AromaCellSequenceFile
  • updateSequences
  • updateSequences.AromaCellSequenceFile
  • updateTargetStrands
  • updateTargetStrands.AromaCellSequenceFile
  • validate.AromaMicroarrayDataSet
  • validate.AromaUnitSignalBinarySet
  • weightedMean
  • whatDataType
  • whatDataType.default
  • writeAxesLayers
  • writeAxesLayers.ChromosomeExplorer
  • writeCopyNumberRegionLayers
  • writeCopyNumberRegionLayers.ChromosomeExplorer
  • writeCytobandLayers
  • writeCytobandLayers.ChromosomeExplorer
  • writeFooter
  • writeGraphs
  • writeGraphs.ChromosomeExplorer
  • writeGridHorizontalLayers
  • writeGridHorizontalLayers.ChromosomeExplorer
  • writeRawCopyNumberLayers
  • writeRawCopyNumberLayers.ChromosomeExplorer
  • writeRawFooter
  • writeRawFooter.AromaTabularBinaryFile
  • writeRegions
  • writeRegions.ChromosomeExplorer
  • writeRegions.CopyNumberSegmentationModel
  • writeRegions.GladModel
  • xMax
  • xMax.RawGenomicSignals
  • xMin
  • xMin.RawGenomicSignals
  • xmlToList
  • xmlToList.character
  • xRange
  • xRange.RawGenomicSignals
  • xSeq
  • xSeq.RawGenomicSignals
  • yellow.colors
  • yMax
  • yMax.RawGenomicSignals
  • yMin
  • yMin.RawGenomicSignals
  • yRange
  • yRange.RawGenomicSignals
  • getDefaultFullName.AromaMicroarrayDataSet
  • getDefaultFullName.AromaTabularBinarySet
  • drawCnRegions.MPCBS
  • extractCopyNumberRegions.MPCBS
  • segmentByMPCBS
  • isCompatibleWith
  • getTags.Arguments
  • getOutputSet
  • getOutputSet.ChromosomalModel
  • setAttributesBy.AromaTabularBinarySet
  • setAttributesBySampleAnnotationFile.AromaTabularBinarySet
  • setAttributesBySampleAnnotationSet.AromaTabularBinarySet
  • setAttributesByTags.AromaTabularBinarySet
  • allocate.AromaCellCpgFile
  • getColumnNames.AromaCellCpgFile
  • getFilenameExtension.AromaCellCpgFile
  • isMissing.AromaCellCpgFile
  • readCpgs
  • readCpgs.AromaCellCpgFile
  • updateCpgs
  • updateCpgs.AromaCellCpgFile
  • getRandomSeed
  • getRandomSeed.CbsModel
  • setRandomSeed
  • setRandomSeed.CbsModel
  • equals.CopyNumberRegions
  • writeDataFrame
  • getParentName
  • getParentName.GenericDataFile
  • getParentName.GenericDataFileSet
  • getRootName
  • getRootName.AromaTabularBinaryFile
  • getRootName.AromaTabularBinarySet
  • getAromaFullNameTranslatorSet
  • getAromaFullNameTranslatorSet.character
  • getFullNameTranslatorSet
  • getFullNameTranslatorSet.character
  • getFullNameTranslatorSet.GenericDataFileSet
  • getAromaFullNameTranslatorSet.AromaMicroarrayDataSet
  • getAromaFullNameTranslatorSet.AromaUnitSignalBinarySet
  • extractRegions
  • extractRegions.RawGenomicSignals
  • subset.CopyNumberRegions
  • writeDataFrame.AromaUnitTotalCnBinarySet
  • writeDataFrame.AromaUnitFracBCnBinarySet
  • -.CopyNumberRegions
  • *.CopyNumberRegions
  • +.CopyNumberRegions
  • getMeanAt
  • getMeanAt.CopyNumberRegions
  • getValueAt
  • getValueAt.CopyNumberRegions
  • prune
  • prune.CopyNumberRegions
  • simulateRawCopyNumbers
  • simulateRawCopyNumbers.CopyNumberRegions
  • xRange.CopyNumberRegions
  • xMax.CopyNumberRegions
  • xMin.CopyNumberRegions
  • append.CopyNumberRegions
  • as.character.SegmentationDataSet
  • byName.CbsSegmentationDataSet
  • byPath.CbsSegmentationDataSet
  • byPath.SegmentationDataSet
  • CbsSegmentationDataFile
  • CbsSegmentationDataSet
  • extractByReferenceName
  • extractByReferenceName.SegmentationDataSet
  • extractBySampleName
  • extractBySampleName.SegmentationDataSet
  • extractCopyNumberRegions.SegmentationDataFile
  • extractCopyNumberRegions.SegmentationDataSet
  • getChipType.SegmentationDataSet
  • getChromosome.SegmentationDataFile
  • getChromosomes.CopyNumberRegions
  • getChromosomes.SegmentationDataSet
  • getDefaultFullName.SegmentationDataSet
  • getReferenceName
  • getReferenceName.SegmentationDataFile
  • getReferenceNames
  • getReferenceNames.SegmentationDataSet
  • getSampleName
  • getSampleName.SegmentationDataFile
  • getSampleNames
  • getSampleNames.SegmentationDataSet
  • loadFit
  • loadFit.CbsSegmentationDataFile
  • loadFit.SegmentationDataFile
  • nbrOfChromosomes
  • nbrOfChromosomes.CopyNumberRegions
  • SegmentationDataFile
  • SegmentationDataSet
  • unique.CopyNumberRegions
  • byGenome
  • byGenome.AromaGenomeTextFile
  • findByGenome
  • findByGenome.AromaGenomeTextFile
  • readDataFrame.AromaGenomeTextFile
  • -.RawGenomicSignals
  • *.RawGenomicSignals
  • +.RawGenomicSignals
  • drawDensity
  • drawDensity.CopyNumberRegions
  • drawDensity.RawGenomicSignals
  • getDensity
  • getDensity.CopyNumberRegions
  • getLength
  • getLength.CopyNumberRegions
  • getOptionalArguments
  • getOptionalArguments.CopyNumberChromosomalModel
  • getChromosomeLength
  • getChromosomeLength.CopyNumberChromosomalModel
  • requireWithMemory
  • requireWithMemory.default
  • writeImage
  • writeImage.Image
  • createImage
  • createImage.matrix
  • getImageData
  • getImageData.Image
  • setImageData
  • setImageData.Image
  • RasterImage
  • [.RasterImage
  • as.character.RasterImage
  • display.RasterImage
  • dropAlpha
  • dropAlpha.RasterImage
  • getImageData.RasterImage
  • read
  • read.RasterImage
  • rescale.RasterImage
  • save.RasterImage
  • setImageData.RasterImage
  • str.RasterImage
  • write.RasterImage
  • writeImage.RasterImage
  • colorize.RasterImage
  • interleave.RasterImage
  • dropRootPathTags.default
  • loadAll
  • loadAll.SampleAnnotationSet
  • byPathnames
  • byPathnames.SampleAnnotationSet
  • getAromaGenomeTextFile
  • getAromaGenomeTextFile.ChromosomalModel
  • getChromosomeLabels
  • getChromosomeLabels.ChromosomeExplorer
  • cat
  • getOption
  • append
  • lapply
  • downloadACS
  • downloadACS.AromaRepository
  • downloadCDF
  • downloadCDF.AromaRepository
  • downloadChipTypeFile
  • downloadProbeSeqsTXT
  • downloadProbeSeqsTXT.AromaRepository
  • downloadTXT
  • downloadTXT.AromaRepository
  • downloadUFL
  • downloadUFL.AromaRepository
  • downloadUGP
  • downloadUGP.AromaRepository
  • getUrlPath
  • getUrlPath.AromaRepository
  • getVerbose.AromaRepository
  • setVerbose.AromaRepository
  • downloadACC
  • downloadACC.AromaRepository
  • downloadACM
  • downloadACM.AromaRepository
  • downloadACP
  • downloadACP.AromaRepository
  • extractPSCNArray
  • extractPSCNArray.AromaUnitTotalCnBinaryFile
  • extractPSCNArray.AromaUnitTotalCnBinarySet
  • extractPSCNMatrix
  • extractPSCNMatrix.AromaUnitTotalCnBinaryFile
  • AromaUcscGenomeTextFile
  • findByGenome.AromaUcscGenomeTextFile
  • getDefaultExtension
  • getDefaultExtension.UnitAnnotationDataFile
  • readDataFrame.AromaUcscGenomeTextFile
  • getDefaultExtension.AromaCellCpgFile
  • getDefaultExtension.AromaCellPositionFile
  • getDefaultExtension.AromaCellSequenceFile
  • getDefaultExtension.AromaUflFile
  • getDefaultExtension.AromaUgpFile
  • plotCoverageMap
  • plotCoverageMap.AromaUgpFile
  • assertOneChromosome
  • assertOneChromosome.RawGenomicSignals
  • getCXY
  • getCXY.RawGenomicSignals
  • getChromosomes.RawGenomicSignals
  • nbrOfChromosomes.RawGenomicSignals
  • extractChromosome
  • extractChromosome.RawGenomicSignals
  • extractChromosomes
  • extractChromosomes.RawGenomicSignals
  • clearCache.RawGenomicSignals
  • clone.RawGenomicSignals
  • getBasicField
  • getBasicField.RawGenomicSignals
  • print.RawGenomicSignals
  • setBasicField
  • setBasicField.RawGenomicSignals
  • newInstance.RawGenomicSignals
  • getDefaultLocusFields
  • getDefaultLocusFields.RawGenomicSignals
  • getVirtualLocusFields
  • getVirtualLocusFields.RawGenomicSignals
  • getVirtualLocusFields.SegmentedGenomicSignalsInterface
  • getVersion.Explorer
  • updateSetupExplorerFile
  • updateSetupExplorerFile.Explorer
  • $.RichDataFrame
  • $<-.RichDataFrame
  • RichDataFrame
  • [.RichDataFrame
  • [[.RichDataFrame
  • [[<-.RichDataFrame
  • as.data.frame.RichDataFrame
  • as.list.RichDataFrame
  • binnedSmoothingByField
  • binnedSmoothingByField.RawGenomicSignals
  • dim.RichDataFrame
  • dropVirtualColumn
  • dropVirtualColumn.RichDataFrame
  • getColumnNames.RichDataFrame
  • getColumnNamesTranslator
  • getColumnNamesTranslator.RichDataFrame
  • getFullName.RichDataFrame
  • getGenericSummary
  • getGenericSummary.RichDataFrame
  • getName.RichDataFrame
  • getSignalColumnName
  • getSignalColumnName.RawGenomicSignals
  • getSignalColumnNames
  • getSignalColumnNames.RawGenomicSignals
  • getSignals.RawCopyNumbers
  • getTags.RichDataFrame
  • getVirtualColumn
  • getVirtualColumn.RichDataFrame
  • getVirtualColumnFunction
  • getVirtualColumnFunction.RichDataFrame
  • getVirtualColumnFunctions
  • getVirtualColumnFunctions.RichDataFrame
  • getVirtualColumnNames
  • getVirtualColumnNames.RichDataFrame
  • getVirtualField
  • getVirtualField.SegmentedGenomicSignalsInterface
  • hasColumn
  • hasColumn.RichDataFrame
  • hasColumns
  • hasColumns.RichDataFrame
  • hasVirtualColumn
  • hasVirtualColumn.RichDataFrame
  • hasVirtualColumns
  • hasVirtualColumns.RichDataFrame
  • length.RichDataFrame
  • names.RichDataFrame
  • newInstance.RichDataFrame
  • print.RichDataFrame
  • rbind.RichDataFrame
  • setAttributes.RichDataFrame
  • setColumnNamesMap
  • setColumnNamesMap.RichDataFrame
  • setColumnNamesTranslator
  • setColumnNamesTranslator.RichDataFrame
  • setName.RichDataFrame
  • setSignals
  • setSignals.RawGenomicSignals
  • setTags.RichDataFrame
  • setVirtualColumn
  • setVirtualColumn.RichDataFrame
  • setVirtualColumnFunctions
  • setVirtualColumnFunctions.RichDataFrame
  • subset.RichDataFrame
  • translateColumnNames.RichDataFrame
  • as.NonPairedPSCNData
  • as.NonPairedPSCNData.NonPairedPSCNData
  • as.NonPairedPSCNData.data.frame
  • as.PairedPSCNData
  • as.PairedPSCNData.NonPairedPSCNData
  • as.PairedPSCNData.PairedPSCNData
  • as.PairedPSCNData.data.frame
  • callNaiveGenotypes.NonPairedPSCNData
  • callNaiveGenotypes.PairedPSCNData
  • callSNPs
  • callSNPs.AbstractPSCNData
  • callSegmentationOutliers
  • callSegmentationOutliers.NonPairedPSCNData
  • callSegmentationOutliers.PairedPSCNData
  • dropSegmentationOutliers
  • dropSegmentationOutliers.NonPairedPSCNData
  • dropSegmentationOutliers.PairedPSCNData
  • extractNonPairedPSCNData
  • extractNonPairedPSCNData.PairedPSCNData
  • findLargeGaps
  • findLargeGaps.AbstractCNData
  • getChipType.AbstractCNData
  • getLocusData
  • getLocusData.AbstractCNData
  • getPlatform.AbstractCNData
  • getSNPFields
  • getSNPFields.AbstractPSCNData
  • getSignalColumnNames.NonPairedPSCNData
  • getSignalColumnNames.PairedPSCNData
  • getTCNs
  • getTCNs.PairedPSCNData
  • getTotalCopyNumbers
  • getTotalCopyNumbers.PairedPSCNData
  • hasKnownPositions
  • hasKnownPositions.AbstractCNData
  • normalizeTumorBoost.PairedPSCNData
  • orderAlongGenome
  • orderAlongGenome.AbstractCNData
  • segmentByCBS.NonPairedPSCNData
  • segmentByCBS.PairedPSCNData
  • segmentByPairedPSCBS
  • segmentByPairedPSCBS.PairedPSCNData
  • setChipType
  • setChipType.AbstractCNData
  • setPlatform
  • setPlatform.AbstractCNData
  • normalizeTumorBoost
  • callNaiveGenotypes
  • getNumberOfFilesAveraged.AromaUnitSignalBinaryFile
  • allocate.AromaUnitPscnBinaryFile
  • byName.AromaUnitPscnBinarySet
  • extractRawCopyNumbers.AromaUnitPscnBinaryFile
  • getAverageFile.AromaUnitPscnBinarySet
  • getColumnNames.AromaUnitPscnBinaryFile
  • hasAlleleBFractions.AromaUnitPscnBinaryFile
  • hasStrandiness.AromaUnitPscnBinaryFile
  • hasTotalCopyNumberRatios
  • hasTotalCopyNumberRatios.AromaUnitPscnBinaryFile
  • writeDataFrame.AromaUnitPscnBinarySet
  • downloadAll
  • downloadAll.AromaRepository
  • listFiles
  • clearCache.AromaRepository
  • findAnnotationDataByChipType.AromaRepository
  • downloadUGC
  • downloadUGC.AromaRepository
  • AromaUnitGcContentFile
  • getColumnNames.AromaUnitGcContentFile
  • getExtensionPattern.AromaUnitGcContentFile
  • getFilenameExtension.AromaUnitGcContentFile
  • AromaUgcFile
  • getReference
  • getReference.CopyNumberChromosomalModel
  • setReference
  • setReference.CopyNumberChromosomalModel
  • getMaxNAFraction
  • getMaxNAFraction.CopyNumberChromosomalModel
  • getDefaultColumnNames.AromaCellCpgFile
  • getDefaultColumnNames.AromaCellPositionFile
  • getDefaultColumnNames.AromaCellSequenceFile
  • getDefaultColumnNames.AromaTabularBinaryFile
  • getDefaultColumnNames.AromaUflFile
  • getDefaultColumnNames.AromaUgpFile
  • getDefaultColumnNames.AromaUnitChromosomeTabularBinaryFile
  • getDefaultColumnNames.AromaUnitGcContentFile
  • getDefaultColumnNames.AromaUnitPscnBinaryFile
  • getParameterSets
  • getParameterSets.ParametersInterface
  • getCacheKey
  • findFilesTodo
  • getParameters
  • write
  • write.default
  • setChromosomes
  • getAlias
  • setAlias
  • process
  • findChangePointsByState
  • findChangePointsByState.SegmentedGenomicSignalsInterface
  • as.character.AromaPlatform
  • equals.AromaPlatform
  • getUnitNames
Documentation reproduced from package aroma.core, version 3.1.3, License: LGPL (>= 2.1)

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