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