The AromaUnitCallSet class
The UnitNamesFile interface class
fitGenotypeConeBySfit.matrix
Fits an affine transformation to allele A and allele B data
The SegmentedCopyNumbers class
Applies patches for a specific package
fit.CopyNumberSegmentationModel
Fits the model
Gets the root path of the output directory
getFullName.AromaTransform
Gets the full name of the output data set
Package aroma.core
getInputDataSet.AromaTransform
Gets the input data set
segmentByCBS.RawGenomicSignals
Segment copy numbers using the CBS method
Generates image files, scripts and dynamic pages for the explorer
Processes the data set
colKernelSmoothing.matrix
Kernel smoothing of a matrix column by column
nbrOfArrays.ChromosomalModel
Gets the number of arrays
getCacheKey.FileCacheKeyInterface
Gets a list of cache key items
Displays the explorer in the default browser
A binary file holding chromosome/position for each cell
The AromaUnitSignalBinarySet class
The CbsModel class
The AbstractPSCNData class
The HaarSegModel class
CopyNumberChromosomalModel
The CopyNumberChromosomalModel class
Gets the name of the output data set
AromaUnitFracBCnBinaryFile
The AromaUnitFracBCnBinaryFile class
The ChromosomeExplorer class
Gets the total number of arrays
getParametersAsString.ParametersInterface
Gets the parameters as character
Gets the tags of the explorer
writeDataFrame.AromaUnitTabularBinaryFile
Writes the data file as a tab-delimited text file
CopyNumberSegmentationModel
The CopyNumberSegmentationModel class
listFiles.AromaRepository
Retrieves the files available on the repository under a particular path
The NonPairedPSCNData class
RawMirroredAlleleBFractions
The RawMirroredAlleleBFractions class
plotTracks.PairedPSCNData
Plots parental specific copy numbers along the genome
The AromaTabularBinarySet class
nbrOfChipTypes.AromaMicroarrayDataSetTuple
Gets the number of chip types
downloadChipTypeFile.AromaRepository
Download a particular chip type annotation file
Sets the alias of the output set
SegmentedAlleleBFractions
The SegmentedAlleleBFractions class
The RawGenomicSignals class
findAnnotationDataByChipType
Locates an annotation data file by its chip type
The ParametersInterface class interface
Gets the path of the output directory
The RawCopyNumbers class
AromaUnitFracBCnBinarySet
The AromaUnitFracBCnBinarySet class
AromaUnitGenotypeCallFile
The AromaUnitGenotypeCallFile class
The AromaGenomeTextFile class
AromaMicroarrayTabularBinaryFile
The AromaMicroarrayTabularBinaryFile class
getModel.ChromosomeExplorer
Gets the model
process.ChromosomeExplorer
Generates image files, scripts and dynamic pages for the explorer
getCacheKey.CacheKeyInterface
Gets a list of cache key items
Gets the names of the input samples
segmentByGLAD.RawGenomicSignals
Segment copy numbers using the GLAD method
AromaUnitTotalCnBinaryFile
The AromaUnitTotalCnBinaryFile class
A binary file holding local CpG density for each cell (probe/feature)
updateSetupExplorerFile.ChromosomeExplorer
Updates the Javascript file
The RawCopyNumberModel class
The RawSequenceReads class
Checks if the data set is processed or not
downloadFile.AromaRepository
Download a particular file from the reposity
getOutputDataSet.AromaTransform
Gets the transformed data set
The AromaPlatform class
segmentByHaarSeg.RawGenomicSignals
Segment copy numbers using the HaarSeg method
The AromaTabularBinaryFile class
Gets the tags of the output data set
Gets the running time of the R process and its children processes
The CacheKeyInterface class interface
The PairedPSCNData class
getRootPath.AromaTransform
Gets the root path of the output directory
fit.CopyNumberChromosomalModel
Fits the model
The AromaMicroarrayDataSet class
The AromaTransform class
Fits an affine transformation to allele A and allele B data
The AromaUnitTypesFile class
AromaUnitSignalBinaryFile
The AromaUnitSignalBinaryFile class
The BinnedScatter class
Non-documented objects
AromaUnitTabularBinaryFile
The AromaUnitTabularBinaryFile class
setArrays.ChromosomeExplorer
Sets the arrays
segmentByMPCBS.RawGenomicSignals
Segment copy numbers using the multi-platform CBS (mpCBS) method
estimateStandardDeviation.RawGenomicSignals
Estimates the standard deviation of the raw Ys
Gets the name of the explorer
The Explorer class
Download a package patch
getChromosomes.ChromosomeExplorer
Gets the chromosomes available
getNames.ChromosomalModel
Gets the names of the arrays
Applies a polishing function to blocks of rows and columns repeatedly
readFooter.AromaTabularBinaryFile
Reads the file footer in XML format into a named nested list
Gets the path of the output directory
getChipType.ChromosomalModel
Gets a label for all chip types merged
The AbstractCNData class
The AromaUnitGenotypeCallSet class
The AromaUnitPscnBinarySet class
The ChromosomalModel class
allocate.AromaTabularBinaryFile
Creates an AromaTabularBinaryFile
SegmentedGenomicSignalsInterface
The SegmentedGenomicSignalsInterface class interface
Gets the indices of units by their names
writeFooter.AromaTabularBinaryFile
Writes a named nested list to the file footer in XML format
fitMultiDimensionalCone.matrix
Fits an affine transformation to multi-dimensional data
AromaMicroarrayDataSetTuple
The AromaMicroarrayDataSetTuple class
estimateSds.CopyNumberChromosomalModel
Estimates the standard deviation of the raw copy numbers (log2-ratios) robustly
getParameters.ParametersInterface
Gets a list of parameters
getChromosomes.ChromosomalModel
Gets the chromosomes available
Creates a Grayscale (TrueColor) Image from a matrix file
The UnitAnnotationDataFile interface class
The AromaRepository class
AromaUnitTotalCnBinarySet
The AromaUnitTotalCnBinarySet class
AromaCellTabularBinaryFile
The AromaCellTabularBinaryFile class
Performs CBS segmentation on a data set
colBinnedSmoothing.matrix
Binned smoothing of a matrix column by column
Merges a list of boxplot.stats() elements
Sets the arrays
The abstract AromaMicroarrayDataFile class
Gets the alias of the output set
The GladModel class
The FileCacheKeyInterface class interface
The RawAlleleBFractions class
Locates an annotation data file
nbrOfChipTypes.ChromosomalModel
Gets the number of chip types
writeDataFrame.AromaUnitSignalBinarySet
Writes the data set as a tab-delimited text file
The AromaUnitPscnBinaryFile class
writeDataFrame.AromaUnitSignalBinaryFile
Writes the data file as a tab-delimited text file
The AromaUnitCallFile class
The UnitTypesFile interface class
extractRawCopyNumbers.CopyNumberChromosomalModel
Extracts relative copy numbers