FirmaModel {aroma.affymetrix}R Documentation

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:
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, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

Author(s)

Ken Simpson (ksimpson[at]wehi.edu.au).


[Package aroma.affymetrix version 1.2.0 Index]