FirmaModel: The FirmaModel class

Description

Package: aroma.affymetrix Class FirmaModel Object ~~| ~~+--Model ~~~~~~~| ~~~~~~~+--UnitModel ~~~~~~~~~~~~| ~~~~~~~~~~~~+--FirmaModel Directly known subclasses: public static class FirmaModel extends UnitModel This class represents the FIRMA (Finding Isoforms using RMA) alternative splicing model.

Usage

FirmaModel(rmaPlm=NULL, summaryMethod=c("median", "upperQuartile", "max"), operateOn=c("residuals", "weights"), ...)

Arguments

rmaPlm

An @RmaPlm object.

summaryMethod

A character specifying what summarization method should be used.

operateOn

A character specifying what statistic to operate on.

...

Arguments passed to constructor of UnitModel.

Fields and Methods

Methods: rll{ calculateResidualSet Gets the set of residuals corresponding to the PLM. calculateWeights - fit Estimates the model parameters. getAsteriskTags - getCdf - getDataSet - getFirmaScores - getFirmaSet Gets the set of FIRMA results for this model. getFitUnitGroupFunction Static method to get the low-level function that fits the PLM. getName - getPlm - getTags - } Methods inherited from UnitModel: findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction Methods inherited from Model: fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags Methods inherited from Object: asThis, getChecksum, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save