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