CbsModel {aroma.core}R Documentation

The CbsModel class


Package: aroma.core
Class CbsModel


Directly known subclasses:

public static class CbsModel
extends CopyNumberSegmentationModel

This class represents the Circular Binary Segmentation (CBS) model [1].


CbsModel(cesTuple=NULL, ..., seed=NULL)



A CopyNumberDataSetTuple.


Arguments passed to the constructor of CopyNumberSegmentationModel.


An (optional) integer that if specified will (temporarily) set the random seed each time before calling the segmentation method. For more information, see segmentByCBS().

Fields and Methods

No methods defined.

Methods inherited from CopyNumberSegmentationModel:
fit, getAsteriskTags, getFitFunction, getFullNames, getRegions, getTags, plot, plotCopyNumberRegionLayers, writeRegions

Methods inherited from CopyNumberChromosomalModel:
as.character, calculateChromosomeStatistics, calculateRatios, estimateSds, extractRawCopyNumbers, fit, getChromosomeLength, getDataFileMatrix, getMaxNAFraction, getNames, getOptionalArguments, getPairedNames, getRefSetTuple, getReference, getReferenceSetTuple, isPaired, newPlot, plotAxesLayers, plotChromosomesLayers, plotCytobandLayers, plotFitLayers, plotGridHorizontalLayers, plotRawCopyNumbers, plotSampleLayers, setReference

Methods inherited from ChromosomalModel:
as.character, fit, getAlias, getAromaGenomeTextFile, getAsteriskTags, getChipType, getChipTypes, getChromosomes, getFullName, getFullNames, getGenome, getGenomeData, getGenomeFile, getListOfAromaUgpFiles, getName, getNames, getParentPath, getPath, getReportPath, getRootPath, getSetTuple, getSets, getTags, indexOf, nbrOfArrays, nbrOfChipTypes, setChromosomes, setGenome

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis


Henrik Bengtsson


[1] Olshen, A. B., Venkatraman, E. S., Lucito, R., Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-572, 2004.
[2] Venkatraman, E. S. & Olshen, A. B. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics, 2007.

See Also


[Package aroma.core version 3.2.2 Index]