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.
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

Henrik Bengtsson