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