ChromosomalModel {aroma.core}

The ChromosomalModel class

Description

Package: aroma.core
Class ChromosomalModel

Object
~~|
~~+--ChromosomalModel

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

public abstract static class ChromosomalModel
extends Object

This abstract class represents a chromosomal model.

Usage

ChromosomalModel(cesTuple=NULL, tags="*", genome="Human", chromosomes=NULL, ...)

Arguments

cesTuple

A AromaMicroarrayDataSetTuple.

tags

A character vector of tags.

genome

A character string specifying what genome is process.

chromosomes

(optional) A vector specifying which chromosomes to process.

...

Not used.

Fields and Methods

Methods:

	fit	-
	getChipType	Gets a label for all chip types merged.
	getChipTypes	-
	getChromosomes	Gets the chromosomes to be processed.
	getFullName	-
	getFullNames	-
	getGenome	-
	getName	-
	getNames	Gets the names of the arrays.
	getPath	-
	getSets	-
	getTags	-
	indexOf	-
	nbrOfArrays	Gets the number of arrays.
	nbrOfChipTypes	Gets the number of chip types.
	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