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.