NmfPlm: The NmfPlm class

In HenrikBengtsson/ACNE: Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

The NmfPlm class

Description

Package: ACNE
Class NmfPlm

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--NmfPlm

Directly known subclasses:
NmfSnpPlm

public abstract static class NmfPlm
extends ProbeLevelModel

This class represents the NMF model of [REF].

Usage

NmfPlm(..., maxIter=10L, maxIterRlm=20L, refs=NULL, flavor=c("v4", "v3", "v2", "v1"))

Arguments

...	Arguments passed to ProbeLevelModel.
maxIter	The maximum number of iteration in the NMF step.
maxIterRlm	A positive integer specifying the maximum number of iterations used in rlm.
refs	An index vector (integer or logical) specifying the reference samples. If NULL, all samples are used as a reference.
flavor	(Internal/developmental only) A character string specifying which algorithm to use.

Fields and Methods

Methods:

	getAsteriskTags	-

Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

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

Author(s)

Henrik Bengtsson

References

[1] M. Ortiz-Estevez, H. Bengtsson, A. Rubio, ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays, Bioinformatics, 2010 [PMC2913655].

See Also

Internally, for each SNP the NMF model is fitted using the fitSnpNmf() function.

HenrikBengtsson/ACNE documentation built on Feb. 20, 2024, 8:20 p.m.