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