aroma.core (version 2.2.2)

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", ...)

Arguments

cesTuple

A AromaMicroarrayDataSetTuple.

tags

A character vector of tags.

genome

A character string specifying what genome is process.

...

Not used.

Fields and Methods

Methods: rll{ clearCache - fit - getAlias - getChipType Gets a label for all chip types merged. getChipTypes - getChromosomes Gets the chromosomes available. getFullName - getFullNames - getGenome - getListOfAromaUgpFiles - getName - getNames Gets the names of the arrays. getParentPath - getPath - getRootPath - getSets - getTags - indexOf - nbrOfArrays Gets the number of arrays. nbrOfChipTypes Gets the number of chip types. setGenome - } Methods inherited from Object: asThis, getChecksum, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

Requirements

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