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