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 publication2016-01-06 10:01:09
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseLGPL (>= 2.1)
Version3.0.0
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

Files in this package

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 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