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