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