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:

	`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, 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

Author

Henrik Bengtsson