CnPlm: The CnPlm class

Description

Package: aroma.affymetrix
Class CnPlm

Interface
~~|
~~+--SnpPlm
~~~~~~~|
~~~~~~~+--CnPlm

Directly known subclasses:
AffineCnPlm, AvgCnPlm, HetLogAddCnPlm, MbeiCnPlm, RmaCnPlm

public class CnPlm
extends SnpPlm

This support class represents a SnpPlm specially designed for copy-number analysis.

Usage

CnPlm(...)

Arguments

...: Arguments passed to SnpPlm.

Methods

Methods:

	`getCellIndices`	-
	`getChipEffectSet`	-
	`getCombineAlleles`	-
	`getProbeAffinityFile`	-
	`setCombineAlleles`	-

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from Interface:
extend, print, uses

Requirements

Classes inheriting from this Interface must provide the following fields, in addition to the ones according to SnpPlm:

combineAlleles: A logical indicating if total or allele-specific copy numbers should be estimated according to the above averaging.

Author

Henrik Bengtsson

Details

Models implementing this copy-number PLM, provides either allele-specific or total copy-number estimates. For allele-specific CNs the underlying SnpPlm model is fitted as is, i.e. for each allele separately with or without the strands first being merged.

For total CNs the probe signals for the two alleles are combined (=summed; not averaged) on the intensity scale before fitting underlying SnpPlm model, again with or without the strands first being merged.