aroma.affymetrix (version 1.3.0)

CopyNumberSegmentationModel: The CopyNumberSegmentationModel class

Description

Package: aroma.affymetrix 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. getRegions - getTags - migrateTool - plot - plotCopyNumberRegionLayers - writeRegions - } Methods inherited from CopyNumberChromosomalModel: as.character, calculateChromosomeStatistics, clearCache, estimateSds, extractRawCopyNumbers, fit, getMatrixChipEffectFiles, getRawCnData, getReferenceSetTuple, getRefSetTuple, isPaired, newPlot, plotAxesLayers, plotChromosomesLayers, plotCytobandLayers, plotFitLayers, plotGridHorizontalLayers, plotRawCopyNumbers, plotSampleLayers Methods inherited from ChromosomalModel: as.character, clearCache, fit, getAlias, getArrays, getAsteriskTags, getChipEffectFiles, getChipType, getChipTypes, getChromosomes, getFullName, getFullNames, getGenome, getGenomeData, getGenomeFile, getListOfAromaUgpFiles, getListOfChipEffectSets, getListOfGenomeInformations, getName, getNames, getParentPath, getPath, getPcuTheta, getPositionChipTypeUnit, getReportPath, getRootPath, getSetTuple, getTableOfArrays, getTags, 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