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