aroma.core (version 3.1.1)

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

refTuple

An optional CopyNumberDataFile, or CopyNumberDataSet or CopyNumberDataSetTuple for pairwise comparisons.

calculateRatios

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

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:

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

Requirements

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