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