CbsModel: The CbsModel class

In aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

The CbsModel class

Description

Package: aroma.core
Class CbsModel

Object
~~|
~~+--ChromosomalModel
~~~~~~~|
~~~~~~~+--CopyNumberChromosomalModel
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CopyNumberSegmentationModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--CbsModel

Directly known subclasses:

public static class CbsModel
extends CopyNumberSegmentationModel

This class represents the Circular Binary Segmentation (CBS) model [1].

Usage

CbsModel(cesTuple=NULL, ..., seed=NULL)

Arguments

cesTuple	A CopyNumberDataSetTuple.
...	Arguments passed to the constructor of CopyNumberSegmentationModel.
seed	An (optional) integer that if specified will (temporarily) set the random seed each time before calling the segmentation method. For more information, see segmentByCBS().

Fields and Methods

Methods:
No methods defined.

Methods inherited from CopyNumberSegmentationModel:
fit, getAsteriskTags, getFitFunction, getFullNames, getRegions, getTags, plot, plotCopyNumberRegionLayers, writeRegions

Methods inherited from CopyNumberChromosomalModel:
as.character, calculateChromosomeStatistics, calculateRatios, estimateSds, extractRawCopyNumbers, fit, getChromosomeLength, getDataFileMatrix, getMaxNAFraction, getNames, getOptionalArguments, getPairedNames, getRefSetTuple, getReference, getReferenceSetTuple, isPaired, newPlot, plotAxesLayers, plotChromosomesLayers, plotCytobandLayers, plotFitLayers, plotGridHorizontalLayers, plotRawCopyNumbers, plotSampleLayers, setReference

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

Author(s)

Henrik Bengtsson

References

[1] Olshen, A. B., Venkatraman, E. S., Lucito, R., Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-572, 2004.
[2] Venkatraman, E. S. & Olshen, A. B. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics, 2007.

See Also

CopyNumberSegmentationModel.

aroma.core documentation built on June 25, 2024, 1:15 a.m.