Package: aroma.core Class CopyNumberSegmentationModel
Object
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ChromosomalModel
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CopyNumberChromosomalModel
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CopyNumberSegmentationModel
Directly known subclasses: CbsModel, GladModel, HaarSegModel
public abstract static class CopyNumberSegmentationModel extends CopyNumberChromosomalModel
This abstract class represents a copy-number segmentation model.
CopyNumberSegmentationModel(...)
Arguments passed to constructor
CopyNumberChromosomalModel
.
Methods:
fit |
Fits the model. | |
getFullNames |
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getRegions |
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getTags |
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plot |
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writeRegions |
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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