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