CopyNumberSegmentationModel: The CopyNumberSegmentationModel class

Description

Package: aroma.core Class CopyNumberSegmentationModel Object ~~| ~~+--ChromosomalModel ~~~~~~~| ~~~~~~~+--CopyNumberChromosomalModel ~~~~~~~~~~~~| ~~~~~~~~~~~~+--CopyNumberSegmentationModel Directly known subclasses: CbsModel, GladModel, HaarSegModel public abstract static class CopyNumberSegmentationModel extends CopyNumberChromosomalModel This abstract class represents a copy-number segmentation model.

Usage

CopyNumberSegmentationModel(...)

Arguments

...

Arguments passed to constructor CopyNumberChromosomalModel.

Fields and Methods

Methods: rll{ fit Fits the model. getFullNames - getRegions - getTags - plot - 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, setGenome

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