CnPlm {aroma.affymetrix} | R Documentation |
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 |
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.
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(s)
Henrik Bengtsson