NmfSnpPlm: The NmfSnpPlm class

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

The NmfSnpPlm class

Description

Package: ACNE
Class NmfSnpPlm

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

Directly known subclasses:

public abstract static class NmfSnpPlm
extends SnpPlm

Usage

NmfSnpPlm(..., mergeStrands=FALSE)

Arguments

...	Arguments passed to NmfPlm.
mergeStrands	If TRUE, the sense and the anti-sense strands are fitted together, otherwise separately.

Fields and Methods

Methods:
No methods defined.

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

Methods inherited from NmfPlm:
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

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