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