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