HaarSegModel {aroma.core} | R Documentation |
Package: aroma.core
Class HaarSegModel
Object
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ChromosomalModel
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CopyNumberChromosomalModel
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CopyNumberSegmentationModel
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HaarSegModel
Directly known subclasses:
public static class HaarSegModel
extends CopyNumberSegmentationModel
This class represents the Haar wavelet-based segmentation (HaarSeg) model [1].
HaarSegModel(cesTuple=NULL, ..., breaksFdrQ=1e-04)
cesTuple |
A CopyNumberDataSetTuple . |
breaksFdrQ |
Default tuning parameters specific to the HaarSeg algorithm. |
... |
Arguments passed to the constructor of
CopyNumberSegmentationModel . |
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
Henrik Bengtsson (http://www.braju.com/R/)
[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