HaarSegModel {aroma.core}R Documentation

The HaarSegModel class

Description

Package: aroma.core
Class HaarSegModel

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

Directly known subclasses:

public static class HaarSegModel
extends CopyNumberSegmentationModel

This class represents the Haar wavelet-based segmentation (HaarSeg) model [1].

Usage

HaarSegModel(cesTuple=NULL, ..., breaksFdrQ=1e-04)

Arguments

cesTuple A CopyNumberDataSetTuple.
breaksFdrQ Default tuning parameters specific to the HaarSeg algorithm.
... Arguments passed to the constructor of CopyNumberSegmentationModel.

Fields and Methods

Methods:
getFitFunction -

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

Methods inherited from CopyNumberChromosomalModel:
as.character, calculateChromosomeStatistics, calculateRatios, clearCache, estimateSds, extractRawCopyNumbers, fit, getDataFileMatrix, getNames, getPairedNames, getReferenceSetTuple, getRefSetTuple, isPaired, newPlot, 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

Author(s)

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

References

[1] Ben-Yaacov E. and Eldar YC. A fast and flexible method for the segmentation of aCGH data, Bioinformatics, 2008. http://www.ee.technion.ac.il/Sites/People/YoninaEldar/Info/software/HaarSeg.htm

See Also

CopyNumberSegmentationModel.


[Package aroma.core version 1.4.0 Index]