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:
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] Ben-Yaacov E. and Eldar YC. A fast and flexible method for the segmentation of aCGH data, Bioinformatics, 2008. https://webee.technion.ac.il/Sites/People/YoninaEldar/software_det1.php

See Also

CopyNumberSegmentationModel.


[Package aroma.core version 3.2.2 Index]