AffineCnPlm: The AffineCnPlm class

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

The AffineCnPlm class

Description

Package: aroma.affymetrix
Class AffineCnPlm

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffinePlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffineSnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CnPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffineCnPlm

Directly known subclasses:

public abstract static class AffineCnPlm
extends CnPlm

Usage

AffineCnPlm(..., combineAlleles=FALSE)

Arguments

...	Arguments passed to AffineSnpPlm.
combineAlleles	If FALSE, allele A and allele B are treated separately, otherwise together.

Fields and Methods

Methods:
No methods defined.

Methods inherited from CnPlm:
getCellIndices, getChipEffectSet, getCombineAlleles, getParameters, getProbeAffinityFile, setCombineAlleles

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

Methods inherited from AffineSnpPlm:
getAsteriskTags

Methods inherited from AffinePlm:
getAsteriskTags, getFitUnitGroupFunction, getProbeAffinityFile

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/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.