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