AbstractCNData
AbstractPSCNData
aCGH
Achim
addBy
addIncludes
addIndexFile
affine
affymetrix
Agilent
al
allocateFromUnitAnnotationDataFile
allocateFromUnitNamesFile
annotationData
anyDuplicated
anyNA
appendColumnNamesTranslator
appendColumnNamesTranslatorBycharacter
appendColumnNamesTranslatorByfunction
appendColumnNamesTranslatorBylist
appendColumnNamesTranslatorByNULL
appendFiles
appendFullNamesTranslator
appendFullNamesTranslatorBydata
appendFullNamesTranslatorByfunction
appendFullNamesTranslatorBylist
appendFullNamesTranslatorByNULL
appendFullNamesTranslatorByTabularTextFile
appendFullNamesTranslatorByTabularTextFileSet
appendFullNameTranslator
appendFullNameTranslatorBycharacter
appendFullNameTranslatorBydata
appendFullNameTranslatorByfunction
appendFullNameTranslatorBylist
appendFullNameTranslatorByNULL
appendFullNameTranslatorByTabularTextFile
appendFullNameTranslatorByTabularTextFileSet
applyBinaryOperator
AppVeyor
AromaCellCpgFile
AromaCellPositionFile
AromaCellSequenceFile
AromaCellTabularBinaryFile
AromaGenomeTextFile
AromaMicroarrayDataFile
AromaMicroarrayDataSet
AromaMicroarrayDataSetTuple
AromaMicroarrayTabularBinaryFile
AromaPlatform
AromaPlatformInterface
AromaRepository
AromaTabularBinaryFile
AromaTabularBinarySet
AromaTransform
AromaUflFile
AromaUgcFile
AromaUgpFile
AromaUnitCallFile
AromaUnitCallSet
AromaUnitFracBCnBinaryFile
AromaUnitFracBCnBinarySet
AromaUnitGcContentFile
AromaUnitGenotypeCallFile
AromaUnitGenotypeCallSet
AromaUnitPscnBinaryFile
AromaUnitPscnBinarySet
AromaUnitSignalBinaryFile
AromaUnitSignalBinarySet
AromaUnitTabularBinaryFile
AromaUnitTotalCnBinaryFile
AromaUnitTotalCnBinarySet
AromaUnitTypesFile
assertDuplicates
assertOneChromosome
asThis
attachLocally
backtransform
BAF
BAFs
Benchmarking
BinnedScatter
binnedSmoothing
binnedSmoothingByField
binnedSmoothingByState
Bioinformatics
Biostatistics
byChipType
byName
byPath
CacheKeyInterface
calculateAverageColumnAcrossFiles
calculateChromosomeStatistics
calculateRatios
callHooks
callSegmentationOutliers
callSNPs
cbind
CbsModel
CGH
ChromosomalModel
ChromosomeExplorer
clearCache
clearColumnNamesTranslator
clearFullNamesTranslator
clearFullNameTranslator
clearListOfColumnNamesTranslators
clearListOfFullNameTranslators
clearLookupCache
CMD
cn
CN
cnRange
colApply
colMeans
colStats
colSums
ColumnNamesInterface
compareChecksum
copynumber
CopyNumberChromosomalModel
CopyNumberDataFile
CopyNumberDataSet
CopyNumberDataSetTuple
CopyNumberSegmentationModel
copyTo
CpG
CRMAv
CxK
DHs
divideBy
DNAcopy
doCBS
drawDensity
droplevels
dropSegmentationOutliers
dropVirtualColumn
dsApply
dsApplyInPairs
DSC
Eldar
eps
estimateSds
estimateStandardDeviation
et
exportAromaUnitPscnBinarySet
expressioncontrol
extractCallArray
extractCalls
extractChromosome
extractChromosomes
extractDataForSegmentation
extractGenotypeMatrix
extractMatrix
extractRawCopyNumbers
extractRawGenomicSignals
extractRawMirroredAlleleBFractions
extractRegion
extractRegions
extractSubset
extractSubsetByState
FileCacheKeyInterface
findByChipType
findByName
findChangePointsByState
findDuplicated
findLargeGaps
findUnitsTodo
Friedrich
fromFile
fullname
FullNameInterface
gaussianSmoothing
GenericDataFile
GenericDataFileSet
GenericDataFileSetList
GenericTabularFile
GenericTabularFileSet
genotypingcontrol
getAlias
getAromaFullNameTranslatorSet
getAromaGenomeTextFile
getAromaPlatform
getAromaUflFile
getAromaUgpFile
getArraysOfInput
getAsteriskTags
getAttribute
getAttributes
getBasicField
getBytesPerColumn
getCacheKey
getChecksum
getChecksumFile
getChecksumFileSet
getChecksumObjects
getChipType
getChipTypes
getChromosome
getChromosomeLength
getChromosomes
getCn
getCNs
getColClasses
getColumnNames
getColumnNamesTranslator
getCommentChar
getCreatedOn
getCXY
getDataFileMatrix
getDefaultColumnClasses
getDefaultColumnClassPatterns
getDefaultColumnNames
getDefaultExtension
getDefaultFullName
getDefaultLocusFields
getEnvironment
getExtension
getExtensionPattern
getFieldModifier
getFieldModifiers
getFields
getFile
getFileClass
getFileList
getFileListClass
getFilename
getFilenameExtension
getFiles
getFileSize
getFileType
getFitFunction
getFullName
getFullNames
getFullNameTranslator
getFullNameTranslatorSet
getGenome
getGenomeData
getGenomeFile
getHeader
getIncludePath
getInstantiationTime
getLastAccessedOn
getLastModifiedOn
getListOfAromaUgpFiles
getListOfColumnNamesTranslators
getListOfFullNameTranslators
getLocusData
getLocusFields
getMainPath
getMaxNAFraction
getName
getNameOfInput
getNames
getNumberOfFilesAveraged
getOneFile
getOptionalArguments
getOutputExtension
getPairedNames
getParameters
getParametersAsString
getParameterSets
getParentName
getParentPath
getPath
getPathname
getPathnames
getPlatform
getPositions
getReadArguments
getReference
getReferenceSetTuple
getRefSetTuple
getRegions
getReportPath
getReportPathPattern
getRootName
getRootPath
getSampleLayerPrefix
getSet
getSets
getSetTuple
getSigma
getSignalColumnName
getSignalColumnNames
getSignals
getSNPFields
getStateColorMap
getStateColors
getStates
getStaticInstance
getSubdirs
getSubname
getTags
getTagsOfInput
getTemplatePath
getUniqueStates
getUnitAnnotationDataFile
getUnitNamesFile
getUnitTypes
getUnitTypesFile
getVersion
getVirtualColumn
getVirtualColumnFunction
getVirtualColumnNames
getVirtualField
getVirtualLocusFields
getWeights
getXScale
getXY
getYScale
GladModel
Grayscale
gunzip
gzip
gzipped
Haar
HaarSeg
HaarSegModel
hasAlleleBFractions
hasBeenModified
hasColumn
hasColumnHeader
hasColumns
hasField
hasFile
hashCode
hasKnownPositions
hasStrandiness
hasTag
hasTags
hasVirtualColumn
hasVirtualColumns
hasWeights
heterozygosity
Hornik
Hupe
Illumina
importFrom
indexOf
Infinium
isAverageFile
isCompatibleWith
isFile
isGzipped
isPaired
Javascript
js
JxI
kernelSmoothing
kernelSmoothingByState
Kx
KxI
KxN
KxNx
Leisch
licence
linkTo
listToXml
logaritmic
Lucito
macOS
mergeBoxplotStats
mpCBS
multiplyBy
na
nbrOfArrays
nbrOfBases
nbrOfChipTypes
nbrOfChromosomes
nbrOfColumns
nbrOfFiles
nbrOfLines
nbrOfLoci
nbrOfRows
nbrOfSets
nbrOfUnits
newInstance
newPlot
NonPairedPSCNData
nonStructure
nucleotides
Nx
NxK
objectSize
oldClass
Olshen
oo
orderAlongGenome
PairedPSCNData
ParametersInterface
Peiffer
plotAxesLayers
plotChromosomesLayers
plotCopyNumberRegionLayers
plotCytobandLayers
plotDensity
plotFitLayers
plotGridHorizontalLayers
plotRawCopyNumbers
plotSampleLayers
pre
Pre
profileCGH
RawAlleleBFractions
RawCopyNumberModel
RawCopyNumbers
RawGenomicSignals
RawMirroredAlleleBFractions
RawSequenceReads
readChecksum
readColumnNames
readColumns
readDataFrame
readFooter
readHeader
readLines
readRawFooter
readRawHeader
redownloaded
renameTo
renameToUpperCaseExt
resequencing
resetFullName
resetFullNames
RichDataFrame
rowsum
segmentByCBS
segmentByGLAD
segmentByHaarSeg
segmentByMPCBS
segmentByPairedPSCBS
SegmentedAlleleBFractions
SegmentedCopyNumbers
SegmentedGenomicSignalsInterface
Seshan
setAlias
setArrays
setAttribute
setAttributes
setAttributesBy
setAttributesBySampleAnnotationFile
setAttributesBySampleAnnotationSet
setAttributesByTags
setBasicField
setChipType
setChromosomes
setColumnNames
setColumnNamesMap
setColumnNamesTranslator
setCommentChar
setExtensionPattern
setFullName
setFullNamesTranslator
setFullNameTranslator
setGenome
setListOfColumnNamesTranslators
setListOfFullNameTranslators
setName
setPlatform
setReference
setReportPathPattern
setSigma
setSignals
setStateColorMap
setStates
setSubname
setTags
setVirtualColumn
setWeights
setXScale
setYScale
signalRange
slotsFromS
sortBy
splitByReportPathPattern
str
subclasses
Subclasses
subname
subtractBy
TabularTextFile
TCN
TCNs
testAttributes
TextUnitNamesFile
translateColumnNames
UnitAnnotationDataFile
UnitNamesFile
UnitTypesFile
unstack
updateColumnNames
updateData
updateDataColumn
updateFullName
updateFullNames
updateSetupExplorerFile
validateChecksum
Venkatraman
Wigler
writeChecksum
writeColumnsToFiles
writeDataFrame
writeFooter
writeRawFooter
writeRegions
xMax
xMin
xRange
xSeq
Yaacov
YC
yMax
yMin
yRange
Ys
Zeileis
