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