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