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