CopyNumberChromosomalModel: The CopyNumberChromosomalModel class
In aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

CopyNumberChromosomalModel

R Documentation

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` 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