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)Default tuning parameters specific to the HaarSeg algorithm.
Arguments passed to the constructor of
CopyNumberSegmentationModel.
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
[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