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