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