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aroma.core (version 2.11.0)

CopyNumberChromosomalModel: The CopyNumberChromosomalModel class

Description

Package: aroma.core Class CopyNumberChromosomalModel Object ~~| ~~+--ChromosomalModel ~~~~~~~| ~~~~~~~+--CopyNumberChromosomalModel Directly known subclasses: CbsModel, CopyNumberSegmentationModel, GladModel, HaarSegModel, RawCopyNumberModel public abstract static class CopyNumberChromosomalModel extends ChromosomalModel This abstract class represents a copy-number model.

Usage

CopyNumberChromosomalModel(cesTuple=NULL, refTuple=NULL, calculateRatios=TRUE, tags="*",
  genome="Human", chromosomes=NULL, maxNAFraction=1/5, ...)

Arguments

cesTuple
A CopyNumberDataSetTuple.
refTuple
An optional CopyNumberDataFile, or CopyNumberDataSet or CopyNumberDataSetTuple
calculateRatios
A logical specifying whether ratios should be calculated relative to the reference. If FALSE, argument refTuple is ignor
tags
A character vector of tags.
genome
A character string specifying what genome is process.
chromosomes
(optional) A vector specifying which chromosomes to process.
maxNAFraction
A double in [0,1] indicating how many non-finite signals are allowed in the sanity checks of the data.
...
Optional arguments that may be used by some of the subclass models.

Fields and Methods

Methods: rll{ extractRawCopyNumbers Extracts relative copy numbers. fit Fits the model. getChromosomeLength - getNames - getReference - isPaired - }

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, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis

Requirements

This class requires genome information annotation files for every chip type.