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