ChromosomalModel {aroma.affymetrix}R Documentation

The ChromosomalModel class

Description

Package: aroma.affymetrix
Class ChromosomalModel

Object
~~|
~~+--ChromosomalModel

Directly known subclasses:
CbsModel, CopyNumberChromosomalModel, CopyNumberSegmentationModel, GladModel, HaarSegModel, RawCopyNumberModel, SmoothMultiarrayModel, SmoothRmaModel, SmoothSaModel

public abstract static class ChromosomalModel
extends Object

This abstract class represents a chromosomal model.

Usage

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

Arguments

cesTuple A ChipEffectSetTuple.
tags A character vector of tags.
genome A character string specifying what genome is process.
... Not used.

Fields and Methods

Methods:
clearCache -
fit -
getAlias -
getArrays Gets the names of the arrays.
getChipEffectFiles -
getChipType Gets a label for all chip types merged.
getChipTypes -
getChromosomes Gets the chromosomes available.
getFullName -
getFullNames -
getGenome -
getListOfAromaUgpFiles -
getListOfChipEffectSets -
getListOfGenomeInformations -
getName -
getNames -
getParentPath -
getPath -
getRootPath -
getTableOfArrays Gets a table of arrays.
getTags -
nbrOfArrays Gets the number of arrays.
nbrOfChipTypes Gets the number of chip types.
setAlias -
setGenome -

Methods inherited from Object:
asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

Requirements

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

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)


[Package aroma.affymetrix version 1.2.0 Index]