  [.AromaTabularBinaryFile [[.AromaTabularBinaryFile
  [<-.AromaTabularBinaryFile addBy addBy.RawGenomicSignals
  addLocusFields addLocusFields.RawGenomicSignals allocate
  allocate.AromaCellSequenceFile
  allocate.AromaMicroarrayTabularBinaryFile allocate.AromaUgpFile
  allocate.AromaUnitCallFile
  allocate.AromaUnitChromosomeTabularBinaryFile
  allocate.AromaUnitGenotypeCallFile allocate.AromaUnitSignalBinaryFile
  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 AromaUgpFile
  AromaUnitChromosomeTabularBinaryFile AromaUnitTotalCnBinaryFileList
  as.character.AromaMicroarrayDataSetTuple
  as.character.AromaMicroarrayTabularBinaryFile
  as.character.AromaTabularBinaryFile as.character.AromaTransform
  as.character.AromaUnitSignalBinaryFile
  as.character.CopyNumberOutliers as.character.CopyNumberRegions
   as.character.RawGenomicSignals
  as.character.TextUnitNamesFile 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
  binScatter binScatter.matrix byChipType
  byChipType.AromaMicroarrayTabularBinaryFile
  byChipType.AromaUnitTabularBinaryFile byChipType.UnitNamesFile
  byName.AromaPlatform byName.AromaUnitFracBCnBinarySet
  byName.AromaUnitGenotypeCallSet byName.AromaUnitSignalBinarySet
  byName.AromaUnitTotalCnBinarySet byPath
  byPath.AromaMicroarrayDataSetTuple calcMargins calcMargins.matrix
  clearCache.AromaTabularBinaryFile clearCache.AromaTransform
  clearCache.AromaUnitChromosomeTabularBinaryFile
  clearCache.AromaUnitTabularBinaryFile 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 CopyNumberOutliers CopyNumberRegions countBases
  countBases.AromaCellSequenceFile countBasesInternal
  countBasesInternal.AromaCellSequenceFile
  dimnames<-.AromaTabularBinaryFile display display.Image divideBy
  divideBy.RawGenomicSignals drawCnRegions drawCnRegions.DNAcopy
  drawCnRegions.HaarSeg drawCnRegions.profileCGH drawCytoband
  drawCytoband.profileCGH drawCytoband2 drawCytoband2.default
  drawLevels drawLevels.CopyNumberOutliers drawLevels.CopyNumberRegions
  estimateStandardDeviation exportTotalCnRatioSet
  exportTotalCnRatioSet.AromaUnitTotalCnBinarySet 
  extractByChromosome
  extractByChromosome.AromaUnitChromosomeTabularBinaryFile
  extractCallArray extractCallArray.AromaUnitCallFile
  extractCallArray.AromaUnitCallSet extractCalls
  extractCalls.AromaUnitCallFile extractCalls.AromaUnitCallSet
  extractCNRs extractCNRs.default extractCopyNumberRegions
  extractCopyNumberRegions.default extractCopyNumberRegions.DNAcopy
  extractCopyNumberRegions.HaarSeg extractCopyNumberRegions.profileCGH
  extractDataForSegmentation
  extractDataForSegmentation.RawGenomicSignals extractGenotypeMatrix
  extractGenotypeMatrix.AromaUnitCallSet
  extractGenotypeMatrix.AromaUnitGenotypeCallFile extractGenotypes
  extractGenotypes.AromaUnitGenotypeCallFile
  extractGenotypes.AromaUnitGenotypeCallSet
  extractMatrix.AromaUnitCallFile
  extractMatrix.AromaUnitSignalBinaryFile extractMergedRawCopyNumbers
  extractMergedRawCopyNumbers.AromaUnitTotalCnBinaryFileList
  extractRawAlleleBFractions extractRawAlleleBFractions.default
  extractRawCNs extractRawCNs.default extractRawCopyNumbers
  extractRawCopyNumbers.AromaUnitTotalCnBinaryFile
  extractRawCopyNumbers.AromaUnitTotalCnBinaryFileList
  extractRawCopyNumbers.default extractRawCopyNumbers.DNAcopy
  extractRawCopyNumbers.HaarSeg extractRawCopyNumbers.profileCGH
  extractRawGenomicSignals
  extractRawGenomicSignals.AromaUnitTotalCnBinaryFileList
  extractRawGenomicSignals.default 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 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 fromFiles.AromaUnitCallSet
  fromFiles.AromaUnitGenotypeCallSet fromPath
  fromPath.SampleAnnotationFile fromPath.SampleAnnotationSet
  gaussianSmoothing gaussianSmoothing.matrix gaussianSmoothing.numeric
  gaussianSmoothing.RawGenomicSignals gaussKernel GenericSummary
  getAlias.AromaMicroarrayDataSetTuple getAromaPlatform
  getAromaPlatform.AromaPlatformInterface getAromaUgpFile
  getAromaUgpFile.AromaPlatform
  getAromaUgpFile.AromaUnitSignalBinaryFile
  getAromaUgpFile.AromaUnitSignalBinarySet
  getAromaUgpFile.UnitNamesFile getArrays getArrayTuple getAsteriskTags
  getAsteriskTags.AromaMicroarrayDataSetTuple
  getAsteriskTags.AromaTransform getAttributeXY
  getAttributeXY.AromaMicroarrayDataFile getBytesPerColumn
  getBytesPerColumn.AromaTabularBinaryFile getChipType
  getChipType.AromaMicroarrayDataFile
  getChipType.AromaMicroarrayDataSet
  getChipType.AromaMicroarrayTabularBinaryFile
  getChipType.AromaUnitSignalBinaryFile
  getChipType.AromaUnitSignalBinarySet getChipType.TextUnitNamesFile
  getChipType.UnitNamesFile getChipTypes
  getChipTypes.AromaMicroarrayDataSetTuple getChromosome
  getChromosome.Arguments getChromosome.RawGenomicSignals
  getChromosomes getChromosomes.Arguments
  getChromosomes.AromaUnitChromosomeTabularBinaryFile getCn
  getCn.RawCopyNumbers getCNs getCNs.RawCopyNumbers getColClasses
  getColClasses.AromaTabularBinaryFile
  getColumnNames.AromaCellSequenceFile
  getColumnNames.AromaTabularBinaryFile getColumnNames.AromaUgpFile
  getColumnNames.AromaUnitChromosomeTabularBinaryFile
  getCommonListElements getCommonPrefix getDeviceResolution
  getDeviceResolution.default getEffects
  getEffects.ProbePositionEffects getFilenameExtension
  getFilenameExtension.AromaCellSequenceFile
  getFilenameExtension.AromaMicroarrayTabularBinaryFile
  getFilenameExtension.AromaUgpFile
  getFilenameExtension.AromaUnitChromosomeTabularBinaryFile
  getFilenameExtension.AromaUnitSignalBinaryFile
  getFilenameExtension.TextUnitNamesFile
  getFullName.AromaMicroarrayDataSetTuple
  getFullNames.AromaMicroarrayDataSetTuple getGenomeVersion
  getGenomeVersion.AromaUnitChromosomeTabularBinaryFile
  getHeaderParameters getHeaderParameters.TextUnitNamesFile getImage
  getImage.matrix getInputDataSet getLabel.AromaMicroarrayDataFile
  getListOfSets getListOfSets.AromaMicroarrayDataSetTuple getLociFields
  getLociFields.RawGenomicSignals getLocusFields
  getLocusFields.RawGenomicSignals getMaxLengthRepeats
  getMaxLengthRepeats.AromaCellSequenceFile
  getName.AromaMicroarrayDataSetTuple getName.AromaPlatform
  getName.RawGenomicSignals getNames.AromaMicroarrayDataSetTuple
  getOutputDataSet getOutputFiles getOutputFiles.AromaTransform
  getParameters.AromaTransform getParametersAsString
  getParametersAsString.AromaTransform getPatterns
  getPatterns.SampleAnnotationFile getPhysicalPositions
  getPhysicalPositions.RawCopyNumbers getPlatform
  getPlatform.AromaMicroarrayDataFile
  getPlatform.AromaMicroarrayDataSet
  getPlatform.AromaMicroarrayTabularBinaryFile
  getPlatform.AromaPlatformInterface
  getPlatform.AromaUnitSignalBinaryFile
  getPlatform.AromaUnitSignalBinarySet getPlatform.TextUnitNamesFile
  getPlatform.UnitNamesFile getPloidy getPloidy.AromaMicroarrayDataFile
  getPositions getPositions.AromaUgpFile getPositions.RawGenomicSignals
  getProbeLength getProbeLength.AromaCellSequenceFile
  getProbePositionEffectDesignMatrix
  getProbePositionEffectDesignMatrix.character
  getProbePositionEffectDesignMatrix.raw getRam getRam.AromaSettings
  getRootPath getRootPath.AromaTransform getSigma
  getSigma.RawGenomicSignals getSignals getSignals.RawGenomicSignals
  getSnpNucleotides getSnpNucleotides.AromaCellSequenceFile
  getSnpPositions getSnpPositions.AromaCellSequenceFile getSnpShifts
  getSnpShifts.AromaCellSequenceFile getStateColors
  getStateColors.SegmentedGenomicSignalsInterface getStates
  setStates.SegmentedGenomicSignalsInterface
  getStates.SegmentedGenomicSignalsInterface getTableOfArrays
  getTags.AromaMicroarrayDataSetTuple getUniqueStates
  getUniqueStates.SegmentedGenomicSignalsInterface getUnitNames
  getUnitNames.TextUnitNamesFile getUnitNames.UnitNamesFile
  getUnitNamesFile getUnitNamesFile.AromaPlatform
  getUnitNamesFile.AromaPlatformInterface getUnitsAt
  getUnitsAt.AromaUgpFile getUnitsOnChromosome
  getUnitsOnChromosome.AromaUgpFile
  getUnitsOnChromosome.AromaUnitChromosomeTabularBinaryFile
  getUnitsOnChromosomes
  getUnitsOnChromosomes.AromaUnitChromosomeTabularBinaryFile
  getVerbose.AromaSettings getWeights getWeights.RawGenomicSignals
  getXScale getXScale.RawGenomicSignals getXY getXY.RawGenomicSignals
  getYScale getYScale.RawGenomicSignals groupBySnpNucleotides
  groupBySnpNucleotides.AromaCellSequenceFile hasAttributeXY
  hasAttributeXY.AromaMicroarrayDataFile hasWeights
  hasWeights.RawGenomicSignals importFrom
  importFrom.AromaTabularBinaryFile importFromGenericTabularFile
  importFromGenericTabularFile.AromaUgpFile importFromTable
  importFromTable.FileMatrix indexOfArrays indexOfColumn
  indexOfColumn.AromaUnitChromosomeTabularBinaryFile indexOfUnits
  indexOfUnits.AromaUnitTabularBinaryFile interleave interleave.Image
  isHeterozygote isHeterozygote.AromaUnitGenotypeCallFile isHomozygote
  isHomozygote.AromaUnitGenotypeCallFile isMissing
  isMissing.AromaCellSequenceFile kernelSmoothing.RawGenomicSignals
  kernelSmoothingByState kernelSmoothingByState.SegmentedGenomicSignalsInterface
  lapply.AromaTabularBinaryFile library lines.CopyNumberOutliers
  lines.CopyNumberRegions lines.RawGenomicSignals listToXml
  listToXml.list locallyUnique locallyUnique.default log2abs log2center
  log2neg log2pos matchPatterns matchPatterns.SampleAnnotationFile
  matrixBlockPolish mergeBoxplotStats mergeByCommonTails multiplyBy
  multiplyBy.RawGenomicSignals nbrOfArrays
  nbrOfArrays.AromaMicroarrayDataSet nbrOfCells
  nbrOfCells.AromaCellTabularBinaryFile nbrOfChipTypes
  nbrOfColumns.AromaTabularBinaryFile nbrOfLoci
  nbrOfLoci.RawGenomicSignals nbrOfRegions
  nbrOfRegions.CopyNumberOutliers nbrOfRegions.CopyNumberRegions
  nbrOfRows.AromaTabularBinaryFile nbrOfUnits
  nbrOfUnits.AromaUnitSignalBinaryFile
  nbrOfUnits.AromaUnitTabularBinaryFile nbrOfUnits.TextUnitNamesFile
  nbrOfUnits.UnitNamesFile norm2d norm2d.matrix normalizeGenotypeCone
  normalizeGenotypeCone.matrix patch patch.AromaPackage
  plot.BinnedScatter plot.ProbePositionEffects plot.RawAlleleBFractions
  plot.RawCopyNumbers plot.RawGenomicSignals plot.SegmentedGenomicSignalsInterface
  points.BinnedScatter points.RawGenomicSignals
  points.SegmentedGenomicSignalsInterface pointsSequence
  pointsSequence.ProbePositionEffects predict.ProbePositionEffects
  print.GenericSummary  process
  readColumns.AromaTabularBinaryFile readData
  readData.SampleAnnotationFile readDataFrame.AromaTabularBinaryFile
  readDataFrame.AromaUnitChromosomeTabularBinaryFile
  readDataFrame.AromaUnitSignalBinaryFile
  readDataFrame.SampleAnnotationFile readFooter readHeader
  readHeader.AromaTabularBinaryFile readNeighborSequenceMatrix
  readNeighborSequenceMatrix.AromaCellSequenceFile
  readPairSequenceMatrix readPairSequenceMatrix.AromaCellSequenceFile
  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.AromaMicroarrayDataSetTuple
  setAttributesBy.AromaMicroarrayDataSet
  setAttributesBySampleAnnotationFile
  setAttributesBySampleAnnotationFile.AromaMicroarrayDataSet
  setAttributesBySampleAnnotationSet
  setAttributesBySampleAnnotationSet.AromaMicroarrayDataSet
  setAttributesByTags.AromaMicroarrayDataFile
  setAttributesByTags.AromaTabularBinaryFile setAttributeXY
  setAttributeXY.AromaMicroarrayDataFile
  setLabel.AromaMicroarrayDataFile setLocusFields
  setLocusFields.RawGenomicSignals setRam setRam.AromaSettings setSigma
  setSigma.RawGenomicSignals setTags.AromaMicroarrayDataSetTuple
  setTags.AromaTransform setVerbose setVerbose.AromaSettings setWeights
  setWeights.RawGenomicSignals setXScale setXScale.RawGenomicSignals
  setYScale setYScale.RawGenomicSignals shakyText shakyText.default
  signalRange signalRange.RawGenomicSignals smoothWRMA
  smoothWRMA.matrix smoothWSA smoothWSA.matrix sort.RawGenomicSignals
  splitByCommonTails sqrtabs sqrtcenter sqrtneg sqrtpos stext
  stext.default 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
  text.ProbePositionEffects textSequence
  textSequence.ProbePositionEffects TextUnitNamesFile updateData
  updateData.AromaTabularBinaryFile updateDataColumn
  updateDataColumn.AromaTabularBinaryFile updateGenotypes
  updateGenotypes.AromaUnitGenotypeCallFile updateSequenceMatrix
  updateSequenceMatrix.AromaCellSequenceFile updateSequences
  updateSequences.AromaCellSequenceFile updateTargetStrands
  updateTargetStrands.AromaCellSequenceFile uses uses.character
   validate.AromaMicroarrayDataSet
  validate.AromaUnitSignalBinarySet weightedMad weightedMean
  whatDataType whatDataType.default writeFooter writeRawFooter
  writeRawFooter.AromaTabularBinaryFile xMax xMax.RawGenomicSignals
  xMin xMin.RawGenomicSignals xmlToList xmlToList.character xRange
  xRange.RawGenomicSignals xSeq xSeq.RawGenomicSignals yellow.colors
All user-level objects in a package should have documentation entries.
 calculateAverageColumnAcrossFiles
 calculateAverageColumnAcrossFiles.GenericTabularFileSet
 lapplyInChunks lapplyInChunks.numeric splitInChunks
 splitInChunks.numeric
  allocate.AromaCellPositionFile AromaCellPositionFile
  byChipType.AromaCellPositionFile getColumnNames.AromaCellPositionFile
  getFilenameExtension.AromaCellPositionFile
  isMissing.AromaCellPositionFile readPositions
  readPositions.AromaCellPositionFile updatePositions
  updatePositions.AromaCellPositionFile

  addIncludes addIncludes.Explorer addIndexFile addIndexFile.Explorer
  as.character.Explorer 
  getAsteriskTags.Explorer getFullName.Explorer
  getIncludePath getIncludePath.Explorer getMainPath
  getMainPath.Explorer getNameOfInput
  getNameOfInput.Explorer getParallelSafe getParallelSafe.Explorer
  getPath.Explorer getReportPathPattern getReportPathPattern.Explorer
  getRootPath.Explorer getSampleLayerPrefix
  getSampleLayerPrefix.Explorer getSubname getSubname.Explorer
  getTagsOfInput getTagsOfInput.Explorer
  getTemplatePath getTemplatePath.Explorer 
  setArrays
  setParallelSafe setParallelSafe.Explorer setReportPathPattern
  setReportPathPattern.Explorer setSubname setSubname.Explorer setup
  setup.Explorer splitByReportPathPattern
  splitByReportPathPattern.Explorer
  getArraysOfInput getArraysOfInput.Explorer
  extractRawAlleleBFractions.AromaUnitFracBCnBinaryFile
  extractRawGenomicSignals.AromaUnitSignalBinaryFile
  extractRawMirroredAlleleBFractions
  extractRawMirroredAlleleBFractions.default
  extractRawMirroredAlleleBFractions.RawAlleleBFractions
 plot.RawMirroredAlleleBFractions 
exportFracBDiffSet exportFracBDiffSet.AromaUnitFracBCnBinarySet
 extractIGV extractIGV.CopyNumberRegions getExpectedOutputFiles
  getExpectedOutputFiles.AromaTransform getOutputDataSet0
  getOutputDataSet0.AromaTransform
 getExpectedOutputFullnames getExpectedOutputFullnames.AromaTransform
 isHeterozygous
isHeterozygous.AromaUnitGenotypeCallFile isHomozygous
isHomozygous.AromaUnitGenotypeCallFile setStates
getStateColorMap getStateColorMap.SegmentedGenomicSignalsInterface
setStateColorMap setStateColorMap.SegmentedGenomicSignalsInterface
 binnedSums binnedSums.RawSequenceReads nbrOfReads
 nbrOfReads.RawSequenceReads plot.RawSequenceReads
  allocateFromUnitAnnotationDataFile
  allocateFromUnitAnnotationDataFile.AromaUnitSignalBinaryFile
  allocateFromUnitAnnotationDataFile.AromaUnitTabularBinaryFile
  byChipType.UnitAnnotationDataFile findUnitTypesFile
  findUnitTypesFile.AromaPlatform
  getAromaUgpFile.UnitAnnotationDataFile
  getChipType.UnitAnnotationDataFile getPlatform.UnitAnnotationDataFile
  getUnitAnnotationDataFile
  getUnitAnnotationDataFile.AromaPlatformInterface getUnitTypes
  getUnitTypes.UnitTypesFile getUnitTypesFile
  getUnitTypesFile.AromaPlatform
  getUnitTypesFile.AromaPlatformInterface
  nbrOfUnits.UnitAnnotationDataFile nbrOfUnits.UnitTypesFile
  allocate.AromaUnitTypesFile
  getChipType.AromaUnitTypesFile getPlatform.AromaUnitTypesFile
  getUnitTypes.AromaUnitTypesFile importFromUnitTypesFile
  importFromUnitTypesFile.AromaUnitTypesFile
extractRawCopyNumbers.RawSequenceReads
yRange yMin yMax
  extractRawCopyNumbers.RawSequenceReads yMax yMax.RawGenomicSignals
  yMin yMin.RawGenomicSignals yRange yRange.RawGenomicSignals
byPath.AromaUnitCallSet byPath.AromaUnitGenotypeCallSet
setName.RawGenomicSignals
  getExtensionPattern.AromaCellPositionFile
  getExtensionPattern.AromaCellSequenceFile
  getExtensionPattern.AromaUgpFile
  getExtensionPattern.AromaUnitSignalBinaryFile
  getExtensionPattern.SampleAnnotationFile
  getExtensionPattern.TextUnitNamesFile
