  [.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 apply apply.default
  apply.SampleAnnotationFile applyBinaryOperator
  applyBinaryOperator.RawGenomicSignals applyRegions
  applyRegions.CopyNumberOutliers applyRows applyRows.CopyNumberRegions
  AromaCellSequenceFile AromaCore AromaPackage
  AromaPlatformInterface 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.AromaCellPositionFile
  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
  clearCache.AromaTabularBinaryFile clearCache.AromaTransform
  clearCache.AromaUnitChromosomeTabularBinaryFile
  clearCache.AromaUnitTabularBinaryFile clearCache.ChromosomalModel
  clearCache.CopyNumberChromosomalModel clearCache.TextUnitNamesFile
  cnRange cnRange.RawCopyNumbers colGaussianSmoothing
  colGaussianSmoothing.matrix colMeans colMeans.AromaTabularBinaryFile
  colMeans.default colMedians.AromaTabularBinaryFile 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 getAromaPlatform.AromaPlatformInterface
  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 getLabel.AromaMicroarrayDataFile
  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.AromaUnitTotalCnBinaryFile
  getNumberOfFilesAveraged.CopyNumberDataFile getOutputDataSet
  getOutputDataSet0 getOutputDataSet0.AromaTransform getOutputFiles
  getOutputFiles.AromaTransform getPairedNames
  getPairedNames.CopyNumberChromosomalModel getParallelSafe
  getParallelSafe.Explorer getParameters.AromaTransform
  getParametersAsString getParametersAsString.AromaTransform
  getParentPath getParentPath.ChromosomalModel getPath.ChromosomalModel
  getPath.ChromosomeExplorer getPath.Explorer getPatterns
  getPatterns.SampleAnnotationFile getPhysicalPositions
  getPhysicalPositions.RawCopyNumbers getPlatform
  getPlatform.AromaMicroarrayDataFile
  getPlatform.AromaMicroarrayDataSet
  getPlatform.AromaMicroarrayTabularBinaryFile
  getPlatform.AromaPlatformInterface
  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.AromaTransform
  getRootPath.ChromosomalModel getRootPath.Explorer 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
  getUnitAnnotationDataFile.AromaPlatformInterface getUnitNames
  getUnitNames.TextUnitNamesFile getUnitNames.UnitNamesFile
  getUnitNamesFile getUnitNamesFile.AromaPlatform
  getUnitNamesFile.AromaPlatformInterface
  getUnitNamesFile.AromaUnitTotalCnBinarySet getUnitsAt
  getUnitsAt.AromaUgpFile getUnitsOnChromosome
  getUnitsOnChromosome.AromaUgpFile
  getUnitsOnChromosome.AromaUnitChromosomeTabularBinaryFile
  getUnitsOnChromosomes
  getUnitsOnChromosomes.AromaUnitChromosomeTabularBinaryFile
  getUnitTypes getUnitTypes.AromaUnitTypesFile
  getUnitTypes.UnitTypesFile getUnitTypesFile
  getUnitTypesFile.AromaPlatform
  getUnitTypesFile.AromaPlatformInterface 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
  lapply.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 nbrOfArrays
  nbrOfArrays.AromaMicroarrayDataSet
  nbrOfArrays.AromaMicroarrayDataSetTuple
  nbrOfArrays.AromaUnitTotalCnBinarySet 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 patch
  patch.AromaPackage plot.BinnedScatter
  plot.CopyNumberSegmentationModel plot.ProbePositionEffects
  plot.profileCGH 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
  process readColumns.AromaTabularBinaryFile readData
  readData.SampleAnnotationFile 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
  setLabel.AromaMicroarrayDataFile 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 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 updateSamplesFile
  updateSequenceMatrix updateSequenceMatrix.AromaCellSequenceFile
  updateSequences updateSequences.AromaCellSequenceFile
  updateTargetStrands updateTargetStrands.AromaCellSequenceFile
  validate.AromaMicroarrayDataSet validate.AromaUnitSignalBinarySet
  weightedMad 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
  getAromaUgpFile.AromaPlatformInterface isCompatibleWith
  isCompatibleWith.AromaPlatformInterface
getTags.Arguments
  doCBS doCBS.CopyNumberDataSet 
  doCBS.CopyNumberDataSetTuple
  getOutputSet
  getOutputSet.ChromosomalModel setAttributesBy.AromaTabularBinarySet
  setAttributesBySampleAnnotationFile.AromaTabularBinarySet
  setAttributesBySampleAnnotationSet.AromaTabularBinarySet
  setAttributesByTags.AromaTabularBinarySet
  allocate.AromaCellCpgFile byChipType.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
  draw draw.density drawDensity drawDensity.CopyNumberRegions
  drawDensity.RawGenomicSignals swapXY swapXY.density
 getDensity getDensity.CopyNumberRegions getLength
 getLength.CopyNumberRegions
getOptionalArguments getOptionalArguments.CopyNumberChromosomalModel
  getChromosomeLength getChromosomeLength.CopyNumberChromosomalModel
requireWithMemory requireWithMemory.default

