CopyNumberChromosomalModel: The CopyNumberChromosomalModel class

Description

Package: aroma.core Class CopyNumberChromosomalModel

Object ~~| ~~+--ChromosomalModel ~~~~~~~| ~~~~~~~+--CopyNumberChromosomalModel

Directly known subclasses: CbsModel, CopyNumberSegmentationModel, GladModel, HaarSegModel, RawCopyNumberModel

public abstract static class CopyNumberChromosomalModel extends ChromosomalModel

This abstract class represents a copy-number model.

Usage

CopyNumberChromosomalModel(cesTuple=NULL, refTuple=NULL, calculateRatios=TRUE, tags="*", genome="Human", chromosomes=NULL, maxNAFraction=1/5, ...)

Arguments

cesTuple

A CopyNumberDataSetTuple.

refTuple

An optional CopyNumberDataFile, or CopyNumberDataSet or CopyNumberDataSetTuple for pairwise comparisons.

calculateRatios

A logical specifying whether ratios should be calculated relative to the reference. If FALSE, argument refTuple is ignored.

Fields and Methods

Methods:

	`extractRawCopyNumbers`
Extracts relative copy numbers.
`fit`	Fits the model.
	`getChromosomeLength`
-
`getNames`	-
	`getReference`
-
`isPaired`	-

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, objectSize, print, save, asThis

Requirements

This class requires genome information annotation files for every chip type.