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