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