CopyNumberChromosomalModel {aroma.core}R Documentation

The CopyNumberChromosomalModel class

Description

Package: aroma.core
Class CopyNumberChromosomalModel

Object
~~|
~~+--ChromosomalModel
~~~~~~~|
~~~~~~~+--CopyNumberChromosomalModel

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

public abstract static class CopyNumberChromosomalModel
extends ChromosomalModel

This abstract class represents a copy-number model.

Usage

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

Arguments

cesTuple A CopyNumberDataSetTuple.
refTuple An optional CopyNumberDataFile, or CopyNumberDataSet or CopyNumberDataSetTuple for pairwise comparisons.
tags A character vector of tags.
genome A character string specifying what genome is process.
... Not used.

Fields and Methods

Methods:
clearCache -
extractRawCopyNumbers Extracts relative copy numbers.
fit Fits the model.
getNames -
getReferenceSetTuple -
isPaired -
plotAxesLayers -
plotChromosomesLayers -
plotCytobandLayers -
plotFitLayers -
plotGridHorizontalLayers -
plotRawCopyNumbers -
plotSampleLayers -

Methods inherited from ChromosomalModel:
as.character, clearCache, fit, getAlias, getAsteriskTags, getChipType, getChipTypes, getChromosomes, getFullName, getFullNames, getGenome, getGenomeData, getGenomeFile, getListOfAromaUgpFiles, getName, getNames, getParentPath, getPath, getReportPath, getRootPath, getSets, getSetTuple, getTags, indexOf, nbrOfArrays, nbrOfChipTypes, 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.core version 1.4.0 Index]