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=3.22.7" 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=3.22.7" 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/camera?package=limma&version=3.22.7" 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=3.22.7" data-mini-rdoc="limma::romer">romer</a></code> </dt><dd>
	Gene set enrichment analysis.</dd>
<dt> <code><a rd-options="" href="/link/ids2indices?package=limma&version=3.22.7" 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=3.22.7" data-mini-rdoc="limma::alias2Symbol">alias2Symbol</a></code> and <code><a rd-options="" href="/link/alias2SymbolTable?package=limma&version=3.22.7" 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/topRomer?package=limma&version=3.22.7" data-mini-rdoc="limma::topRomer">topRomer</a></code> </dt><dd>
	Display results from romer tests as a top-table.</dd>
<dt> <code><a rd-options="" href="/link/geneSetTest?package=limma&version=3.22.7" data-mini-rdoc="limma::geneSetTest">geneSetTest</a></code> or <code><a rd-options="" href="/link/wilcoxGST?package=limma&version=3.22.7" 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=3.22.7" data-mini-rdoc="limma::barcodeplot">barcodeplot</a></code> </dt><dd>
	Enrichment plot of a gene set.</dd>

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='camera'>camera</a></code> </dt><dd>
	Competitive gene set testing.</dd>


<dt> <code><a rd-options='' href='romer'>romer</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='topRomer'>topRomer</a></code> </dt><dd>
	Display results from romer tests as a top-table.</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>

</dl>

10.GeneSetTests: Topic: Gene Set Tests

Description

Arguments