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