GOthresh

retrieve lines of m that meet both enrichThresh and countThresh

In gene-expression microarray studies, for example, one generally obtains a list of
dozens or hundreds of genes that differ in expression between samples and then asks
'What does all of this mean biologically?' Alternatively, gene lists can be derived conceptually
in addition to experimentally. For instance, one might want to analyze a group of genes known
as housekeeping genes. The work of the Gene Ontology (GO) Consortium <geneontology.org>
provides a way to address that question. GO organizes genes into hierarchical categories based
on biological process, molecular function and subcellular localization. The role of 'GoMiner'
is to automate the mapping between a list of genes and GO, and to provide a statistical
summary of the results as well as a visualization.

Barry Zeeberg

GoMiner

Automate the Mapping Between a List of Genes and Gene Ontology
Categories

GOthresh function

<dl><dt>m</dt>
<dd>return value of GOenrich3()</dd>
<dt>sampleFDR</dt>
<dd>component of return value of RCPD()</dd>
<dt>enrichThresh</dt>
<dd>numerical acceptance threshold for enrichment</dd>
<dt>countThresh</dt>
<dd>numerical acceptance threshold for gene count</dd>
<dt>pvalThresh</dt>
<dd>numerical acceptance threshold for pval</dd>
<dt>fdrThresh</dt>
<dd>numerical acceptance threshold for fdr</dd></dl>

Arguments

GOthresh — GOthresh

<dl>

<dt>m</dt>
<dd>return value of GOenrich3()</dd>


<dt>sampleFDR</dt>
<dd>component of return value of RCPD()</dd>


<dt>enrichThresh</dt>
<dd>numerical acceptance threshold for enrichment</dd>


<dt>countThresh</dt>
<dd>numerical acceptance threshold for gene count</dd>


<dt>pvalThresh</dt>
<dd>numerical acceptance threshold for pval</dd>


<dt>fdrThresh</dt>
<dd>numerical acceptance threshold for fdr</dd>

</dl>

GOthresh: GOthresh

Description

Usage

Value

Arguments

Examples