Package: aroma.core Class CbsModel
Object
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~~+--ChromosomalModel
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~~~~~~~+--CopyNumberChromosomalModel
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~~~~~~~~~~~~+--CopyNumberSegmentationModel
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~~~~~~~~~~~~~~~~~+--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)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().
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
[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.