aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

Core methods and classes used by higher-level aroma.* packages part of the Aroma Project, e.g. aroma.affymetrix and aroma.cn.

AuthorHenrik Bengtsson [aut, cre, cph], Mark Robinson [ctb], Ken Simpson [ctb]
Date of publication2017-03-23 13:10:08 UTC
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseLGPL (>= 2.1)
Version3.1.0
https://github.com/HenrikBengtsson/aroma.core, http://www.aroma-project.org/

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Man pages

AbstractCNData: The AbstractCNData class

AbstractPSCNData: The AbstractPSCNData class

allocate.AromaTabularBinaryFile: Creates an AromaTabularBinaryFile

AromaCellCpgFile: A binary file holding local CpG density for each cell...

AromaCellPositionFile: A binary file holding chromosome/position for each cell

AromaCellTabularBinaryFile: The AromaCellTabularBinaryFile class

aroma.core-package: Package aroma.core

AromaGenomeTextFile: The AromaGenomeTextFile class

AromaMicroarrayDataFile: The abstract AromaMicroarrayDataFile class

AromaMicroarrayDataSet: The AromaMicroarrayDataSet class

AromaMicroarrayDataSetTuple: The AromaMicroarrayDataSetTuple class

AromaMicroarrayTabularBinaryFile: The AromaMicroarrayTabularBinaryFile class

AromaPlatform: The AromaPlatform class

AromaPlatformInterface: The AromaPlatformInterface class

AromaRepository: The AromaRepository class

AromaTabularBinaryFile: The AromaTabularBinaryFile class

AromaTabularBinarySet: The AromaTabularBinarySet class

AromaTransform: The AromaTransform class

AromaUnitCallFile: The AromaUnitCallFile class

AromaUnitCallSet: The AromaUnitCallSet class

AromaUnitFracBCnBinaryFile: The AromaUnitFracBCnBinaryFile class

AromaUnitFracBCnBinarySet: The AromaUnitFracBCnBinarySet class

AromaUnitGenotypeCallFile: The AromaUnitGenotypeCallFile class

AromaUnitGenotypeCallSet: The AromaUnitGenotypeCallSet class

AromaUnitPscnBinaryFile: The AromaUnitPscnBinaryFile class

AromaUnitPscnBinarySet: The AromaUnitPscnBinarySet class

AromaUnitSignalBinaryFile: The AromaUnitSignalBinaryFile class

AromaUnitSignalBinarySet: The AromaUnitSignalBinarySet class

AromaUnitTabularBinaryFile: The AromaUnitTabularBinaryFile class

AromaUnitTotalCnBinaryFile: The AromaUnitTotalCnBinaryFile class

AromaUnitTotalCnBinarySet: The AromaUnitTotalCnBinarySet class

AromaUnitTypesFile: The AromaUnitTypesFile class

as.GrayscaleImage.matrix: Creates a Grayscale (Color) Image from a matrix file

BinnedScatter: The BinnedScatter class

CacheKeyInterface: The CacheKeyInterface class interface

CbsModel: The CbsModel class

ChromosomalModel: The ChromosomalModel class

ChromosomeExplorer: The ChromosomeExplorer class

colBinnedSmoothing.matrix: Binned smoothing of a matrix column by column

colKernelSmoothing.matrix: Kernel smoothing of a matrix column by column

CopyNumberChromosomalModel: The CopyNumberChromosomalModel class

CopyNumberSegmentationModel: The CopyNumberSegmentationModel class

display.Explorer: Displays the explorer in the default browser

doCBS: Performs Circular Binary Segmentation (CBS) on a data set

downloadChipTypeFile.AromaRepository: Download a particular chip type annotation file

downloadFile.AromaRepository: Download a particular file from the reposity

estimateSds.CopyNumberChromosomalModel: Estimates the standard deviation of the raw copy numbers...

estimateStandardDeviation.RawGenomicSignals: Estimates the standard deviation of the raw Ys

Explorer: The Explorer class

exportAromaUnitPscnBinarySet: Export total and allele B signal data sets as a unified...

extractRawCopyNumbers.CopyNumberChromosomalModel: Extracts relative copy numbers

FileCacheKeyInterface: The FileCacheKeyInterface class interface

findAnnotationData: Locates an annotation data file

findAnnotationDataByChipType: Locates an annotation data file by its chip type

findFilesTodo.AromaTransform: Finds files in the data set still not processed

fit.CopyNumberChromosomalModel: Fits the model

fit.CopyNumberSegmentationModel: Fits the model

fitGenotypeConeBySfit.matrix: Fits an affine transformation to allele A and allele B data

fitGenotypeCone.matrix: Fits an affine transformation to allele A and allele B data

fitMultiDimensionalCone.matrix: Fits an affine transformation to multi-dimensional data

getAlias.Explorer: Gets the alias of the output set

getAromaPlatform.AromaPlatformInterface: Gets the platform

getCacheKey.CacheKeyInterface: Gets a list of cache key items

getCacheKey.FileCacheKeyInterface: Gets a list of cache key items

getChipType.AromaPlatformInterface: Gets the chip type

getChipType.ChromosomalModel: Gets a label for all chip types merged

getChromosomes.ChromosomalModel: Gets the chromosomes to be processed

getChromosomes.ChromosomeExplorer: Gets the chromosomes available

getFullName.AromaTransform: Gets the full name of the output data set

getInputDataSet.AromaTransform: Gets the input data set

getModel.ChromosomeExplorer: Gets the model

getName.AromaTransform: Gets the name of the output data set

getName.Explorer: Gets the name of the explorer

getNames.ChromosomalModel: Gets the names of the arrays

getNames.Explorer: Gets the names of the input samples

getOutputDataSet.AromaTransform: Gets the transformed data set

getParametersAsString.ParametersInterface: Gets the parameters as character

getParameters.ParametersInterface: Gets a list of parameters

getPath.AromaTransform: Gets the path of the output directory

getPath.Explorer: Gets the path of the output directory

getPlatform.AromaPlatformInterface: Gets the platform

getRootPath.AromaTransform: Gets the root path of the output directory

getRootPath.Explorer: Gets the root path of the output directory

getTags.AromaTransform: Gets the tags of the output data set

getTags.Explorer: Gets the tags of the explorer

getUnitAnnotationDataFile.AromaPlatformInterface: Gets a unit annotation data file of a particular class

GladModel: The GladModel class

HaarSegModel: The HaarSegModel class

indexOf.UnitNamesFile: Gets the indices of units by their names

isCompatibleWith.AromaPlatformInterface: Checks if a particular unit annotation data file is...

isDone.AromaTransform: Checks if the data set is processed or not

listFiles.AromaRepository: Retrieves the files available on the repository under a...

matrixBlockPolish.matrix: Applies a polishing function to blocks of rows and columns...

mergeBoxplotStats.list: Merges a list of boxplot.stats() elements

nbrOfArrays.ChromosomalModel: Gets the number of arrays

nbrOfArrays.Explorer: Gets the total number of arrays

nbrOfChipTypes.AromaMicroarrayDataSetTuple: Gets the number of chip types

nbrOfChipTypes.ChromosomalModel: Gets the number of chip types

Non-documented_objects: Non-documented objects

NonPairedPSCNData: The NonPairedPSCNData class

PairedPSCNData: The PairedPSCNData class

ParametersInterface: The ParametersInterface class interface

plotTracks.PairedPSCNData: Plots parental specific copy numbers along the genome

process.AromaTransform: Processes the data set

process.ChromosomeExplorer: Generates image files, scripts and dynamic pages for the...

process.Explorer: Generates image files, scripts and dynamic pages for the...

processTime: Gets the running time of the R process and its children...

RawAlleleBFractions: The RawAlleleBFractions class

RawCopyNumberModel: The RawCopyNumberModel class

RawCopyNumbers: The RawCopyNumbers class

RawGenomicSignals: The RawGenomicSignals class

RawMirroredAlleleBFractions: The RawMirroredAlleleBFractions class

RawSequenceReads: The RawSequenceReads class

readFooter.AromaTabularBinaryFile: Reads the file footer in XML format into a named nested list

segmentByCBS.RawGenomicSignals: Segment copy numbers using the CBS method

segmentByGLAD.RawGenomicSignals: Segment copy numbers using the GLAD method

segmentByHaarSeg.RawGenomicSignals: Segment copy numbers using the HaarSeg method

segmentByMPCBS.RawGenomicSignals: Segment copy numbers using the multi-platform CBS (mpCBS)...

SegmentedAlleleBFractions: The SegmentedAlleleBFractions class

SegmentedCopyNumbers: The SegmentedCopyNumbers class

SegmentedGenomicSignalsInterface: The SegmentedGenomicSignalsInterface class interface

setAlias.Explorer: Sets the alias of the output set

setArrays.ChromosomeExplorer: Sets the arrays

setArrays.Explorer: Sets the arrays

UnitAnnotationDataFile: The UnitAnnotationDataFile interface class

UnitNamesFile: The UnitNamesFile interface class

UnitTypesFile: The UnitTypesFile interface class

updateSetupExplorerFile.ChromosomeExplorer: Updates the Javascript file

writeDataFrame.AromaUnitSignalBinaryFile: Writes the data file as a tab-delimited text file

writeDataFrame.AromaUnitSignalBinarySet: Writes the data set as a tab-delimited text file

writeDataFrame.AromaUnitTabularBinaryFile: Writes the data file as a tab-delimited text file

writeFooter.AromaTabularBinaryFile: Writes a named nested list to the file footer in XML format

Functions

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

Files

aroma.core
aroma.core/inst
aroma.core/inst/annotationData
aroma.core/inst/annotationData/genomes
aroma.core/inst/annotationData/genomes/Human
aroma.core/inst/annotationData/genomes/Human/Human,cytobands,hg17,GLADv2.4.0,HB20100219.txt
aroma.core/inst/annotationData/genomes/Human/Human,chromosomes.txt
aroma.core/inst/annotationData/genomes/Canine
aroma.core/inst/annotationData/genomes/Canine/Canine,chromosomes,UGP,HB20100822.txt
aroma.core/inst/annotationData/genomes/Mouse
aroma.core/inst/annotationData/genomes/Mouse/Mouse,chromosomes.txt
aroma.core/inst/bin
aroma.core/inst/bin/nohupR
aroma.core/inst/testScripts
aroma.core/inst/testScripts/fileFormats
aroma.core/inst/testScripts/fileFormats/acf
aroma.core/inst/testScripts/fileFormats/acf/test20090518,acf.R
aroma.core/inst/testScripts/fileFormats/acf/test20090107,AromaUnitGenotypeCallSet.R
aroma.core/inst/testScripts/fileFormats/acf/test20090105,acf.R
aroma.core/inst/testScripts/fileFormats/acs
aroma.core/inst/testScripts/fileFormats/acs/test20080804,acs.R
aroma.core/inst/testScripts/system
aroma.core/inst/testScripts/system/CnSegmentation
aroma.core/inst/testScripts/system/CnSegmentation/test20090510,SEG.Rex
aroma.core/inst/testScripts/system/CnSegmentation/test20090510,SEG,weighted.Rex
aroma.core/inst/testScripts/system/CnSegmentation/test20100222,SEG,symmetry.Rex
aroma.core/inst/testScripts/system/RawGenomicSignals
aroma.core/inst/testScripts/system/RawGenomicSignals/test20090510,Ops.Rex
aroma.core/inst/testScripts/system/RawGenomicSignals/test20090628,binSmoothing.Rex
aroma.core/inst/testScripts/system/RawGenomicSignals/test20090628,binSmoothingByState.Rex
aroma.core/inst/testScripts/system/UGP
aroma.core/inst/testScripts/system/UGP/test20090508,UGP.Rex
aroma.core/inst/testScripts/system/RawAlleleBFractions
aroma.core/inst/testScripts/system/RawAlleleBFractions/test20090510,FracB.Rex
aroma.core/inst/reports
aroma.core/inst/reports/includes
aroma.core/inst/reports/includes/images
aroma.core/inst/reports/includes/images/pixelWhite.png
aroma.core/inst/reports/includes/images/indicator.gif
aroma.core/inst/reports/includes/images/indicator_medium.gif
aroma.core/inst/reports/includes/css
aroma.core/inst/reports/includes/css/R.css
aroma.core/inst/reports/includes/css/ChromosomeExplorer.css
aroma.core/inst/reports/includes/css/ArrayExplorer.css
aroma.core/inst/reports/includes/css/rsp.css
aroma.core/inst/reports/includes/css/figures.css
aroma.core/inst/reports/includes/js
aroma.core/inst/reports/includes/js/domUtils.js
aroma.core/inst/reports/includes/js/Webcuts.js
aroma.core/inst/reports/includes/js/require.js
aroma.core/inst/reports/includes/js/ArrayExplorer
aroma.core/inst/reports/includes/js/ArrayExplorer/ArrayExplorer.js
aroma.core/inst/reports/includes/js/ArrayExplorer/HISTORY
aroma.core/inst/reports/includes/js/ScrollImage2d.js
aroma.core/inst/reports/includes/js/ChromosomeExplorer
aroma.core/inst/reports/includes/js/ChromosomeExplorer/ChromosomeExplorer.js
aroma.core/inst/reports/includes/js/ChromosomeExplorer/HISTORY
aroma.core/inst/reports/includes/js/Scrollbar2d.js
aroma.core/inst/reports/templates
aroma.core/inst/reports/templates/rsp
aroma.core/inst/reports/templates/rsp/ArrayExplorer
aroma.core/inst/reports/templates/rsp/ArrayExplorer/setupExplorer.js.rsp
aroma.core/inst/reports/templates/rsp/ChromosomeExplorer
aroma.core/inst/reports/templates/rsp/ChromosomeExplorer/setupExplorer.js.rsp
aroma.core/inst/reports/templates/html
aroma.core/inst/reports/templates/html/ArrayExplorer
aroma.core/inst/reports/templates/html/ArrayExplorer/about.html
aroma.core/inst/reports/templates/html/ArrayExplorer/ArrayExplorer.html
aroma.core/inst/reports/templates/html/ArrayExplorer/help.html
aroma.core/inst/reports/templates/html/ChromosomeExplorer
aroma.core/inst/reports/templates/html/ChromosomeExplorer/index.html
aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer.html
aroma.core/inst/reports/templates/html/ChromosomeExplorer/help.html
aroma.core/tests
aroma.core/tests/RichDataFrame.R
aroma.core/tests/binScatter.R
aroma.core/tests/RawGenomicSignals.R
aroma.core/tests/colKernelSmoothing.R
aroma.core/tests/RawGenomicSignals.SEG.R
aroma.core/tests/aromaSettings.R
aroma.core/tests/PairedPSCNData.R
aroma.core/tests/RawCopyNumbers.R
aroma.core/tests/matrixBlockPolish.R
aroma.core/tests/mergeBoxplotStats.R
aroma.core/tests/PairedPSCNData,SEG.R
aroma.core/tests/colBinnedSmoothing.R
aroma.core/tests/fitMultiDimensionalCone.R
aroma.core/tests/fitGenotypeCone.R
aroma.core/tests/SegmentedCopyNumbers.R
aroma.core/tests/RawGenomicSignals.SEG,MP.R
aroma.core/tests/RawCopyNumbers,states.R
aroma.core/NAMESPACE
aroma.core/NEWS
aroma.core/R
aroma.core/R/CopyNumberRegions.EXT.R aroma.core/R/mergeBoxplotStats.list.R aroma.core/R/AromaPlatformInterface.R aroma.core/R/AromaUnitGenotypeCallSet.R aroma.core/R/ChromosomalModel.drawCytoband.R aroma.core/R/AromaUnitPscnBinarySet.R aroma.core/R/RichDataFrame.R aroma.core/R/SampleAnnotationFile.R aroma.core/R/lapplyInChunks.R aroma.core/R/AromaUnitChromosomeTabularBinaryFile.R aroma.core/R/RawGenomicSignals.segmentByGLAD.R aroma.core/R/AromaUnitTotalCnBinarySet.R aroma.core/R/CbsSegmentationDataFile.R aroma.core/R/AromaMicroarrayDataFile.ATTRS.R aroma.core/R/SampleAnnotationSet.R aroma.core/R/CopyNumberRegions.R aroma.core/R/fitGenotypeCone.matrix.R aroma.core/R/TextUnitNamesFile.R aroma.core/R/AromaUnitTotalCnBinaryFile.extractPSCNArray.R aroma.core/R/simpleXml.R aroma.core/R/private.Machine.R aroma.core/R/findAnnotationData.R aroma.core/R/RawGenomicSignals.segmentByMPCBS.R aroma.core/R/CopyNumberOutliers.R aroma.core/R/000.R aroma.core/R/RawMirroredAlleleBFractions.R aroma.core/R/AromaUgpFile.R aroma.core/R/SegmentationDataSet.R aroma.core/R/AromaCellSequenceFile.R aroma.core/R/AromaMicroarrayDataSet.ATTRS.R aroma.core/R/AromaUnitSignalBinarySet.writeDataFrame.R aroma.core/R/Explorer.R aroma.core/R/getAromaFullNameTranslatorSet.R aroma.core/R/AromaSettings.R aroma.core/R/AromaMicroarrayDataSet.R aroma.core/R/AromaUnitSignalBinarySet.R aroma.core/R/AromaUnitTabularBinaryFile.R aroma.core/R/fitSplineBlockPolish.matrix.R aroma.core/R/GLAD.EXTS.R aroma.core/R/RawGenomicSignals.segmentByHaarSeg.R aroma.core/R/profileCGH.plotProfile2.R aroma.core/R/AromaUnitSignalBinaryFile.writeDataFrame.R aroma.core/R/RawGenomicSignals.R aroma.core/R/AromaPlatform.R aroma.core/R/ProbePositionEffects.R aroma.core/R/processTime.R aroma.core/R/AromaUflFile.R aroma.core/R/colKernelSmoothing.R aroma.core/R/008.BioC.R aroma.core/R/doCBS.R aroma.core/R/AromaUnitTypesFile.R aroma.core/R/backtransformMultiDimensionalCone.matrix.R aroma.core/R/BasicObject.asThis.R aroma.core/R/CopyNumberSegmentationModel.plotCopyNumberRegionLayers.R aroma.core/R/999.DEPRECATED.R aroma.core/R/convertTable.R aroma.core/R/stextChipType.R aroma.core/R/AromaUnitTotalCnBinaryFileList.R aroma.core/R/AromaUnitFracBCnBinarySet.R aroma.core/R/smoothWRMA.matrix.R aroma.core/R/009.setup.R aroma.core/R/AromaTransform.R aroma.core/R/CopyNumberChromosomalModel.R aroma.core/R/AromaUnitTotalCnBinarySetTuple.R aroma.core/R/CopyNumberSegmentationModel.R aroma.core/R/kernelWeights.R aroma.core/R/AromaUnitCallFile.R aroma.core/R/AromaCellTabularBinaryFile.R aroma.core/R/998.AromaPackage.R aroma.core/R/AromaUnitTabularBinaryFile.writeDataFrame.R aroma.core/R/ChromosomeExplorer.R aroma.core/R/RawGenomicSignals.SEG.R aroma.core/R/SegmentedGenomicSignalsInterface.R aroma.core/R/DNAcopy.EXTS.R aroma.core/R/smoothWSA.matrix.R aroma.core/R/AromaMicroarrayDataFile.R aroma.core/R/findAnnotationDataByChipType.R aroma.core/R/ChromosomalModel.R aroma.core/R/RasterImage.R aroma.core/R/backtransformGenotypeCone.matrix.R aroma.core/R/AromaUnitGcContentFile.R aroma.core/R/PairedPSCNData.R aroma.core/R/RawCopyNumbers.R aroma.core/R/fitWHRCModel.matrix.R aroma.core/R/AromaUnitTotalCnBinaryFile.R aroma.core/R/AromaTabularBinaryFile.R aroma.core/R/normalizeGenotypeCone.R aroma.core/R/getDeviceResolution.R aroma.core/R/HaarSegModel.R aroma.core/R/RawSequenceReads.R aroma.core/R/CopyNumberChromosomalModel.plotSampleLayers.R aroma.core/R/AromaUgpFile.plotCoverageMap.R aroma.core/R/RawGenomicSignals.segmentByCBS.R aroma.core/R/BinnedScatter.R aroma.core/R/RawCopyNumberModel.R aroma.core/R/Image.EXTS.R aroma.core/R/CopyNumberRegions.EXT2.R aroma.core/R/AromaMicroarrayDataFile.PLOT.R aroma.core/R/locallyUnique.R aroma.core/R/UnitAnnotationDataFile.R aroma.core/R/UnitTypesFile.R aroma.core/R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R aroma.core/R/yellow.colors.R aroma.core/R/NonPairedPSCNData.R aroma.core/R/colBinnedSmoothing.R aroma.core/R/matrixBlockPolish.matrix.R aroma.core/R/drawCytoband2.R aroma.core/R/stringTree.R aroma.core/R/AromaRepository.R aroma.core/R/RawGenomicSignals.OPS.R aroma.core/R/requireWithMemory.R aroma.core/R/AromaUnitPscnBinaryFile.R aroma.core/R/CbsSegmentationDataSet.R aroma.core/R/fitMultiDimensionalCone.matrix.R aroma.core/R/SegmentedAlleleBFracions.R aroma.core/R/profileCGH.plotRawCNs.R aroma.core/R/AromaUnitTotalCnBinaryFile.xam.R aroma.core/R/getCommonListElements.R aroma.core/R/GladModel.R aroma.core/R/006.fixVarArgs.R aroma.core/R/AromaCellSequenceFile.REPEATS.R aroma.core/R/SegmentedCopyNumbers.R aroma.core/R/RawGenomicSignals.append.R aroma.core/R/profileCGH.drawExtraAnnotations.R aroma.core/R/AromaMicroarrayDataSet.EXT.R aroma.core/R/AromaMicroarrayTabularBinaryFile.R aroma.core/R/GenericDataFileSet.getParentName.R aroma.core/R/RawSequenceReads.EXTRAS.R aroma.core/R/AromaTabularBinarySet.ATTRS.R aroma.core/R/AromaUnitFracBCnBinarySet.exportFracBDiffSet.R aroma.core/R/GenericTabularFileSet.calculateAverageColumnAcrossFiles.R aroma.core/R/remap.R aroma.core/R/AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R aroma.core/R/AromaUnitFracBCnBinaryFile.R aroma.core/R/999.AromaCore.R aroma.core/R/SegmentationDataFile.R aroma.core/R/AromaUnitSignalBinaryFile.R aroma.core/R/RawAlleleBFractions.R aroma.core/R/AromaCellCpgFile.R aroma.core/R/AbstractPSCNData.R aroma.core/R/AromaCellPositionFile.R aroma.core/R/UnitNamesFile.R aroma.core/R/fitWRMA.matrix.R aroma.core/R/PairedPSCNData.PLOT.R aroma.core/R/Arguments.EXTRAS.R aroma.core/R/AromaMicroarrayDataSetTuple.R aroma.core/R/SegmentedGenomicSignalsInterface.COLS.R aroma.core/R/CopyNumberChromosomalModel.plotChromosomesLayers.R aroma.core/R/AromaGenomeTextFile.R aroma.core/R/CopyNumberOutliers.FOREIGN.R aroma.core/R/AromaUnitGenotypeCallFile.R aroma.core/R/AromaCellSequenceFile.SNPs.R aroma.core/R/CopyNumberChromosomalModel.plotRawCopyNumbers.R aroma.core/R/ChromosomeExplorer.LAYERS.R aroma.core/R/HaarSeg.EXTS.R aroma.core/R/ParametersInterface.R aroma.core/R/CopyNumberChromosomalModel.newPlot.R aroma.core/R/norm2d.matrix.R aroma.core/R/999.NonDocumentedObjects.R aroma.core/R/999.package.R aroma.core/R/library.patch.R aroma.core/R/GladModel.onFitAddGenotypeCalls.R aroma.core/R/shakyText.R aroma.core/R/RawGenomicSignals.PLOT.R aroma.core/R/findPngDevice.R aroma.core/R/transforms.R aroma.core/R/CopyNumberChromosomalModel.plotFitLayers.R aroma.core/R/AbstractCNData.R aroma.core/R/AromaNnn.getRootName.R aroma.core/R/fitWHLAPLM.matrix.R aroma.core/R/CopyNumberDataSetTuple.R aroma.core/R/zzz.R aroma.core/R/AromaUcscGenomeTextFile.R aroma.core/R/CbsModel.R aroma.core/R/CopyNumberSegmentationModel.plot.R aroma.core/R/AromaUnitCallSet.R aroma.core/R/CopyNumberRegions.PLOT.R aroma.core/R/getProbePositionEffectDesignMatrix.R aroma.core/R/AromaTabularBinarySet.R aroma.core/R/colGaussianSmoothing.R aroma.core/R/MPCBS.EXTS.R aroma.core/R/CacheKeyInterface.R aroma.core/R/FileCacheKeyInterface.R
aroma.core/MD5
aroma.core/DESCRIPTION
aroma.core/man
aroma.core/man/getFullName.AromaTransform.Rd aroma.core/man/getNames.Explorer.Rd aroma.core/man/downloadFile.AromaRepository.Rd aroma.core/man/display.Explorer.Rd aroma.core/man/Explorer.Rd aroma.core/man/BinnedScatter.Rd aroma.core/man/CopyNumberSegmentationModel.Rd aroma.core/man/getPath.Explorer.Rd aroma.core/man/RawAlleleBFractions.Rd aroma.core/man/getCacheKey.CacheKeyInterface.Rd aroma.core/man/fit.CopyNumberChromosomalModel.Rd aroma.core/man/getRootPath.AromaTransform.Rd aroma.core/man/getChromosomes.ChromosomeExplorer.Rd aroma.core/man/AromaUnitFracBCnBinarySet.Rd aroma.core/man/process.ChromosomeExplorer.Rd aroma.core/man/getCacheKey.FileCacheKeyInterface.Rd aroma.core/man/indexOf.UnitNamesFile.Rd aroma.core/man/AromaTransform.Rd aroma.core/man/getUnitAnnotationDataFile.AromaPlatformInterface.Rd aroma.core/man/GladModel.Rd aroma.core/man/CacheKeyInterface.Rd aroma.core/man/fit.CopyNumberSegmentationModel.Rd aroma.core/man/writeDataFrame.AromaUnitSignalBinarySet.Rd aroma.core/man/downloadChipTypeFile.AromaRepository.Rd aroma.core/man/nbrOfChipTypes.AromaMicroarrayDataSetTuple.Rd aroma.core/man/segmentByHaarSeg.RawGenomicSignals.Rd aroma.core/man/estimateSds.CopyNumberChromosomalModel.Rd aroma.core/man/fitGenotypeCone.matrix.Rd aroma.core/man/getChipType.ChromosomalModel.Rd aroma.core/man/getModel.ChromosomeExplorer.Rd aroma.core/man/findAnnotationDataByChipType.Rd aroma.core/man/getAromaPlatform.AromaPlatformInterface.Rd aroma.core/man/writeDataFrame.AromaUnitSignalBinaryFile.Rd aroma.core/man/AromaUnitCallSet.Rd aroma.core/man/nbrOfArrays.ChromosomalModel.Rd aroma.core/man/getParametersAsString.ParametersInterface.Rd aroma.core/man/exportAromaUnitPscnBinarySet.Rd aroma.core/man/AbstractPSCNData.Rd aroma.core/man/AromaRepository.Rd aroma.core/man/AromaUnitPscnBinaryFile.Rd aroma.core/man/segmentByGLAD.RawGenomicSignals.Rd aroma.core/man/FileCacheKeyInterface.Rd aroma.core/man/getRootPath.Explorer.Rd aroma.core/man/segmentByCBS.RawGenomicSignals.Rd aroma.core/man/nbrOfArrays.Explorer.Rd aroma.core/man/findFilesTodo.AromaTransform.Rd aroma.core/man/getInputDataSet.AromaTransform.Rd aroma.core/man/RawMirroredAlleleBFractions.Rd aroma.core/man/HaarSegModel.Rd aroma.core/man/AromaUnitPscnBinarySet.Rd aroma.core/man/allocate.AromaTabularBinaryFile.Rd aroma.core/man/aroma.core-package.Rd aroma.core/man/AromaUnitTypesFile.Rd aroma.core/man/AromaUnitSignalBinaryFile.Rd aroma.core/man/getOutputDataSet.AromaTransform.Rd aroma.core/man/getNames.ChromosomalModel.Rd aroma.core/man/AromaUnitTabularBinaryFile.Rd aroma.core/man/CopyNumberChromosomalModel.Rd aroma.core/man/isCompatibleWith.AromaPlatformInterface.Rd aroma.core/man/AromaPlatformInterface.Rd aroma.core/man/estimateStandardDeviation.RawGenomicSignals.Rd aroma.core/man/fitGenotypeConeBySfit.matrix.Rd aroma.core/man/AromaMicroarrayDataFile.Rd aroma.core/man/setArrays.ChromosomeExplorer.Rd aroma.core/man/processTime.Rd aroma.core/man/getChromosomes.ChromosomalModel.Rd aroma.core/man/plotTracks.PairedPSCNData.Rd aroma.core/man/getTags.Explorer.Rd aroma.core/man/AromaCellPositionFile.Rd aroma.core/man/isDone.AromaTransform.Rd aroma.core/man/doCBS.Rd aroma.core/man/getPlatform.AromaPlatformInterface.Rd aroma.core/man/AromaPlatform.Rd aroma.core/man/SegmentedGenomicSignalsInterface.Rd aroma.core/man/AromaUnitSignalBinarySet.Rd aroma.core/man/mergeBoxplotStats.list.Rd aroma.core/man/RawCopyNumberModel.Rd aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd aroma.core/man/findAnnotationData.Rd aroma.core/man/CbsModel.Rd aroma.core/man/ChromosomeExplorer.Rd aroma.core/man/updateSetupExplorerFile.ChromosomeExplorer.Rd aroma.core/man/RawGenomicSignals.Rd aroma.core/man/extractRawCopyNumbers.CopyNumberChromosomalModel.Rd aroma.core/man/writeDataFrame.AromaUnitTabularBinaryFile.Rd aroma.core/man/ParametersInterface.Rd aroma.core/man/getAlias.Explorer.Rd aroma.core/man/ChromosomalModel.Rd aroma.core/man/AromaUnitCallFile.Rd aroma.core/man/AromaUnitGenotypeCallFile.Rd aroma.core/man/UnitTypesFile.Rd aroma.core/man/getName.AromaTransform.Rd aroma.core/man/setArrays.Explorer.Rd aroma.core/man/nbrOfChipTypes.ChromosomalModel.Rd aroma.core/man/AromaUnitGenotypeCallSet.Rd aroma.core/man/setAlias.Explorer.Rd aroma.core/man/AromaMicroarrayDataSet.Rd aroma.core/man/getTags.AromaTransform.Rd aroma.core/man/segmentByMPCBS.RawGenomicSignals.Rd aroma.core/man/fitMultiDimensionalCone.matrix.Rd aroma.core/man/getPath.AromaTransform.Rd aroma.core/man/NonPairedPSCNData.Rd aroma.core/man/AromaUnitTotalCnBinaryFile.Rd aroma.core/man/UnitNamesFile.Rd aroma.core/man/AromaTabularBinarySet.Rd aroma.core/man/readFooter.AromaTabularBinaryFile.Rd aroma.core/man/colKernelSmoothing.matrix.Rd aroma.core/man/process.AromaTransform.Rd aroma.core/man/getChipType.AromaPlatformInterface.Rd aroma.core/man/AromaCellTabularBinaryFile.Rd aroma.core/man/AromaMicroarrayDataSetTuple.Rd aroma.core/man/getParameters.ParametersInterface.Rd aroma.core/man/colBinnedSmoothing.matrix.Rd aroma.core/man/AromaCellCpgFile.Rd aroma.core/man/matrixBlockPolish.matrix.Rd aroma.core/man/RawSequenceReads.Rd aroma.core/man/as.GrayscaleImage.matrix.Rd aroma.core/man/PairedPSCNData.Rd aroma.core/man/AromaGenomeTextFile.Rd aroma.core/man/listFiles.AromaRepository.Rd aroma.core/man/AbstractCNData.Rd aroma.core/man/process.Explorer.Rd aroma.core/man/UnitAnnotationDataFile.Rd aroma.core/man/AromaTabularBinaryFile.Rd aroma.core/man/writeFooter.AromaTabularBinaryFile.Rd aroma.core/man/AromaUnitTotalCnBinarySet.Rd aroma.core/man/SegmentedCopyNumbers.Rd aroma.core/man/RawCopyNumbers.Rd aroma.core/man/getName.Explorer.Rd aroma.core/man/AromaUnitFracBCnBinaryFile.Rd aroma.core/man/Non-documented_objects.Rd aroma.core/man/SegmentedAlleleBFractions.Rd

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