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

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

Author
Henrik Bengtsson [aut, cre, cph], Mark Robinson [ctb], Ken Simpson [ctb]
Date of publication
2016-01-06 10:01:09
Maintainer
Henrik Bengtsson <henrikb@braju.com>
License
LGPL (>= 2.1)
Version
3.0.0
URLs

View on CRAN

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
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