aroma.core (version 2.8.0)

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", maxNAFraction=1/5, ...)

Arguments

cesTuple

A CopyNumberDataSetTuple.

refTuple

An optional CopyNumberDataFile, or CopyNumberDataSet or CopyNumberDataSetTup

calculateRatios

A logical specifying whether ratios should be calculated relative to the reference. If FALSE, argument refTuple is i

tags

A character vector of tags.

genome

A character string specifying what genome is 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, getSets, getSetTuple, getTags, indexOf, nbrOfArrays, nbrOfChipTypes, setGenome Methods inherited from Object: asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

Requirements

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