ChromosomalModel: 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.

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, objectSize, print, save, asThis

Requirements

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