CopyNumberChromosomalModel {aroma.core} | R Documentation |
Package: aroma.core
Class CopyNumberChromosomalModel
Object
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ChromosomalModel
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CopyNumberChromosomalModel
Directly known subclasses:
CbsModel, CopyNumberSegmentationModel, GladModel, HaarSegModel, RawCopyNumberModel
public abstract static class CopyNumberChromosomalModel
extends ChromosomalModel
This abstract class represents a copy-number model.
CopyNumberChromosomalModel(cesTuple=NULL, refTuple=NULL, tags="*", genome="Human", ...)
cesTuple |
A CopyNumberDataSetTuple . |
refTuple |
An optional CopyNumberDataFile ,
or CopyNumberDataSet or CopyNumberDataSetTuple
for pairwise comparisons. |
tags |
A character vector of tags. |
genome |
A character string specifying what genome is process. |
... |
Not used. |
Methods:
clearCache | - | |
extractRawCopyNumbers | Extracts relative copy numbers. | |
fit | Fits the model. | |
getNames | - | |
getReferenceSetTuple | - | |
isPaired | - | |
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
This class requires genome information annotation files for every chip type.
Henrik Bengtsson (http://www.braju.com/R/)