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