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