AffineCnPlm: 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 seperately, 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, getParameterSet, 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, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis