AlleleSummation

A <code><a href="/link/SnpChipEffectSet?package=aroma.affymetrix&version=2.5.0" rd-options="" data-mini-rdoc="aroma.affymetrix::SnpChipEffectSet">SnpChipEffectSet</a></code>.

dataSet

If <code><a href="/link/TRUE?package=aroma.affymetrix&version=2.5.0&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, missing values are excluded when summing
 the signals from the two alleles.

ignoreNAs

Arguments passed to <code><a href="/link/UnitModel?package=aroma.affymetrix&version=2.5.0" rd-options="" data-mini-rdoc="aroma.affymetrix::UnitModel">UnitModel</a></code>.

Package: aroma.affymetrix Class AlleleSummation<code><a href="/link/Object?package=aroma.affymetrix&version=2.5.0&to=R.oo" rd-options="R.oo" data-mini-rdoc="R.oo::Object">Object</a></code><code>~~|</code><code>~~+--</code><code><a href="/link/Model?package=aroma.affymetrix&version=2.5.0&to=aroma.affymetrix" rd-options="aroma.affymetrix" data-mini-rdoc="aroma.affymetrix::Model">Model</a></code><code>~~~~~~~|</code><code>~~~~~~~+--</code><code><a href="/link/UnitModel?package=aroma.affymetrix&version=2.5.0&to=aroma.affymetrix" rd-options="aroma.affymetrix" data-mini-rdoc="aroma.affymetrix::UnitModel">UnitModel</a></code><code>~~~~~~~~~~~~|</code><code>~~~~~~~~~~~~+--</code><code>AlleleSummation</code>Directly known subclasses:public abstract static class AlleleSummationextends <a href="/link/UnitModel?package=aroma.affymetrix&version=2.5.0&to=aroma.affymetrix" rd-options="aroma.affymetrix" data-mini-rdoc="aroma.affymetrix::UnitModel">UnitModel</a>This class takes allele-specific chip effect estimates of a
 SnpChipEffectSet and returns a CnChipEffectSet holding the summed
 allele estimates.

classes

This package implements classes for files and sets of
        files for various Affymetrix file formats, e.g.
        AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet.
        These are designed to be memory efficient but still being fast.
        The idea is to keep all data on file and only read data into
        memory when needed.  Clever caching mechanisms are used to
        minimize the overhead of data IO.  All of the above is hidden
        in the package API and for the developer (and the end user),
        the data is queried as if it lives in memory.  With this design
        it is only the diskspace that limits the number of arrays that
        can be analyzed.  To install, do:
        source("http://www.aroma-project.org/hbLite.R");
        hbInstall("aroma.affymetrix").

Henrik Bengtsson

aroma.affymetrix

Analysis of large Affymetrix microarray data sets

AlleleSummation function

Methods:<tabular>rll</tabular>{
 	<code>findUnitsTodo</code> 	-	<code>getAsteriskTags</code> 	-	<code><a href="/link/getChipEffectSet?package=aroma.affymetrix&version=2.5.0&to=aroma.affymetrix%3AgetChipEffectSet.AlleleSummation" rd-options="aroma.affymetrix:getChipEffectSet.AlleleSummation" data-mini-rdoc="aroma.affymetrix:getChipEffectSet.AlleleSummation::getChipEffectSet">getChipEffectSet</a></code> 	Gets the set of chip effects for this model.	<code>process</code> 	-}


 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, $, $&lt;-, [[, [[&lt;-, 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

AlleleSummation: The AlleleSummation class

Description

Usage

Arguments

Fields and Methods