CbsModel {aroma.core} | R Documentation |
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, ...)
cesTuple |
A CopyNumberDataSetTuple . |
... |
Arguments passed to the constructor of
CopyNumberSegmentationModel . |
Methods:
getFitFunction | - |
Methods inherited from CopyNumberSegmentationModel:
fit, getAsteriskTags, getFitFunction, getFullNames, getRegions, getTags, plot, plotCopyNumberRegionLayers, writeRegions
Methods inherited from CopyNumberChromosomalModel:
as.character, calculateChromosomeStatistics, calculateRatios, clearCache, estimateSds, extractRawCopyNumbers, fit, getDataFileMatrix, getNames, getPairedNames, getReferenceSetTuple, getRefSetTuple, isPaired, newPlot, plotAxesLayers, plotChromosomesLayers, plotCytobandLayers, plotFitLayers, plotGridHorizontalLayers, plotRawCopyNumbers, plotSampleLayers
Methods inherited from ChromosomalModel:
as.character, clearCache, fit, getAlias, getAsteriskTags, getChipType, getChipTypes, getChromosomes, getFullName, getFullNames, getGenome, getGenomeData, getGenomeFile, getListOfAromaUgpFiles, getName, getNames, getParentPath, getPath, getReportPath, getRootPath, getSets, getSetTuple, getTags, indexOf, nbrOfArrays, nbrOfChipTypes, setAlias, setGenome
Methods inherited from Object:
asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save
Henrik Bengtsson (http://www.braju.com/R/)
[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.