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