10.GeneSetTests

This page gives an overview of the LIMMA functions for gene set testing and pathway analysis.<dl>
<dt> <code><a rd-options="" href="/link/roast?package=limma&version=3.28.14" data-mini-rdoc="limma::roast">roast</a></code> </dt><dd>
	Self-contained gene set testing for one set.</dd></dl>
<dt> <code><a rd-options="" href="/link/mroast?package=limma&version=3.28.14" data-mini-rdoc="limma::mroast">mroast</a></code> </dt><dd>
	Self-contained gene set testing for many sets.</dd>
<dt> <code><a rd-options="" href="/link/fry?package=limma&version=3.28.14" data-mini-rdoc="limma::fry">fry</a></code> </dt><dd>
	Fast approximation to <code>mroast</code>, especially useful when heteroscedasticity of genes can be ignored.</dd>
<dt> <code><a rd-options="" href="/link/camera?package=limma&version=3.28.14" data-mini-rdoc="limma::camera">camera</a></code> </dt><dd>
	Competitive gene set testing.</dd>
<dt> <code><a rd-options="" href="/link/romer?package=limma&version=3.28.14" data-mini-rdoc="limma::romer">romer</a></code> and <code><a rd-options="" href="/link/topRomer?package=limma&version=3.28.14" data-mini-rdoc="limma::topRomer">topRomer</a></code> </dt><dd>
	Gene set enrichment analysis.</dd>
<dt> <code><a rd-options="" href="/link/ids2indices?package=limma&version=3.28.14" data-mini-rdoc="limma::ids2indices">ids2indices</a></code> </dt><dd>
	Convert gene sets consisting of vectors of gene identifiers into a list of indices suitable for use in the above functions.</dd>
<dt> <code><a rd-options="" href="/link/alias2Symbol?package=limma&version=3.28.14" data-mini-rdoc="limma::alias2Symbol">alias2Symbol</a></code> and <code><a rd-options="" href="/link/alias2SymbolTable?package=limma&version=3.28.14" data-mini-rdoc="limma::alias2SymbolTable">alias2SymbolTable</a></code> </dt><dd>
	Convert gene symbols or aliases to current official symbols.</dd>
<dt> <code><a rd-options="" href="/link/geneSetTest?package=limma&version=3.28.14" data-mini-rdoc="limma::geneSetTest">geneSetTest</a></code> or <code><a rd-options="" href="/link/wilcoxGST?package=limma&version=3.28.14" data-mini-rdoc="limma::wilcoxGST">wilcoxGST</a></code> </dt><dd>
	Simple gene set testing based on gene or probe permutation.</dd>
<dt> <code><a rd-options="" href="/link/barcodeplot?package=limma&version=3.28.14" data-mini-rdoc="limma::barcodeplot">barcodeplot</a></code> </dt><dd>
	Enrichment plot of a gene set.</dd>
<dt> <code><a rd-options="" href="/link/goana?package=limma&version=3.28.14" data-mini-rdoc="limma::goana">goana</a></code> and <code><a rd-options="" href="/link/topGO?package=limma&version=3.28.14" data-mini-rdoc="limma::topGO">topGO</a></code></dt><dd>
	Gene ontology over-representation analysis of gene lists using Entrez Gene IDs.
	<code>goana</code> can work directly on a fitted model object or on one or more lists of genes.</dd>
<dt> <code><a rd-options="" href="/link/kegga?package=limma&version=3.28.14" data-mini-rdoc="limma::kegga">kegga</a></code> and <code><a rd-options="" href="/link/topKEGG?package=limma&version=3.28.14" data-mini-rdoc="limma::topKEGG">topKEGG</a></code></dt><dd>
	KEGG pathway over-representation analysis of gene lists using Entrez Gene IDs.
	<code>kegga</code> can work directly on a fitted model object or on one or more lists of genes.</dd>

documentation

Data analysis, linear models and differential expression for microarray data.

Gordon Smyth

limma

Linear Models for Microarray Data

10.GeneSetTests function

This page gives an overview of the LIMMA functions for gene set testing and pathway analysis.

<dl>
<dt> <code><a rd-options='' href='roast'>roast</a></code> </dt><dd>
	Self-contained gene set testing for one set.</dd>


<dt> <code><a rd-options='' href='mroast'>mroast</a></code> </dt><dd>
	Self-contained gene set testing for many sets.</dd>


<dt> <code><a rd-options='' href='fry'>fry</a></code> </dt><dd>
	Fast approximation to <code>mroast</code>, especially useful when heteroscedasticity of genes can be ignored.</dd>


<dt> <code><a rd-options='' href='camera'>camera</a></code> </dt><dd>
	Competitive gene set testing.</dd>


<dt> <code><a rd-options='' href='romer'>romer</a></code> and <code><a rd-options='' href='topRomer'>topRomer</a></code> </dt><dd>
	Gene set enrichment analysis.</dd>


<dt> <code><a rd-options='' href='ids2indices'>ids2indices</a></code> </dt><dd>
	Convert gene sets consisting of vectors of gene identifiers into a list of indices suitable for use in the above functions.</dd>


<dt> <code><a rd-options='' href='alias2Symbol'>alias2Symbol</a></code> and <code><a rd-options='' href='alias2SymbolTable'>alias2SymbolTable</a></code> </dt><dd>
	Convert gene symbols or aliases to current official symbols.</dd>


<dt> <code><a rd-options='' href='geneSetTest'>geneSetTest</a></code> or <code><a rd-options='' href='wilcoxGST'>wilcoxGST</a></code> </dt><dd>
	Simple gene set testing based on gene or probe permutation.</dd>


<dt> <code><a rd-options='' href='barcodeplot'>barcodeplot</a></code> </dt><dd>
	Enrichment plot of a gene set.</dd>


<dt> <code><a rd-options='' href='goana'>goana</a></code> and <code><a rd-options='' href='topGO'>topGO</a></code></dt><dd>
	Gene ontology over-representation analysis of gene lists using Entrez Gene IDs.
	<code>goana</code> can work directly on a fitted model object or on one or more lists of genes.</dd>


<dt> <code><a rd-options='' href='kegga'>kegga</a></code> and <code><a rd-options='' href='topKEGG'>topKEGG</a></code></dt><dd>
	KEGG pathway over-representation analysis of gene lists using Entrez Gene IDs.
	<code>kegga</code> can work directly on a fitted model object or on one or more lists of genes.</dd>

</dl>

10.GeneSetTests: Topic: Gene Set Tests

Description

Arguments

See Also