CopyNumberChromosomalModel {aroma.core}

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.

tags

A character vector of tags.

genome

A character string specifying what genome is process.

chromosomes

(optional) A vector specifying which chromosomes to process.

maxNAFraction

A double in [0,1] indicating how many non-finite signals are allowed in the sanity checks of the data.

...

Optional arguments that may be used by some of the subclass models.

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, names, objectSize, print, save, asThis

Requirements

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

Author(s)

Henrik Bengtsson