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aroma.affymetrix (version 1.3.0)

CopyNumberChromosomalModel: The CopyNumberChromosomalModel class

Description

Package: aroma.affymetrix 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 ChipEffectSetTuple.
refTuple
An optional ChipEffectSetTuple for pairwise comparisons.
tags
A character vector of tags.
genome
A character string specifying what genome is process.
...
Not used.

Fields and Methods

Methods: rll{ clearCache - extractRawCopyNumbers - fit Fits the model. getReferenceSetTuple - isPaired - plotAxesLayers - plotChromosomesLayers - plotCytobandLayers - plotFitLayers - plotGridHorizontalLayers - plotRawCopyNumbers - plotSampleLayers - } Methods inherited from ChromosomalModel: as.character, clearCache, fit, getAlias, getArrays, getAsteriskTags, getChipEffectFiles, getChipType, getChipTypes, getChromosomes, getFullName, getFullNames, getGenome, getGenomeData, getGenomeFile, getListOfAromaUgpFiles, getListOfChipEffectSets, getListOfGenomeInformations, getName, getNames, getParentPath, getPath, getPcuTheta, getPositionChipTypeUnit, getReportPath, getRootPath, getSetTuple, getTableOfArrays, getTags, 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.