runGoMinerExamples

driver to run GoMiner under several randomization procedures

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

runGoMinerExamples function

<dl><dt>title</dt>
<dd>character string descriptive title</dd>
<dt>dir</dt>
<dd>character string full pathname to the directory acting result repository</dd>
<dt>sampleList</dt>
<dd>character list of gene names</dd>
<dt>GOGOA3</dt>
<dd>return value of subsetGOGOA()</dd>
<dt>ontology</dt>
<dd>character string c("molecular_function", "cellular_component", "biological_process")</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>
<dt>nrand</dt>
<dd>numeric number of randomizations to compute FDR</dd>
<dt>mn</dt>
<dd>integer param passed to trimGOGOA3, min size threshold for a category</dd>
<dt>mx</dt>
<dd>integer param passed to trimGOGOA3, max size threshold for a category</dd>
<dt>verbose</dt>
<dd>integer vector representing classes</dd></dl>

Arguments

runGoMinerExamples — runGoMinerExamples

<dl>

<dt>title</dt>
<dd>character string descriptive title</dd>


<dt>dir</dt>
<dd>character string full pathname to the directory acting result repository</dd>


<dt>sampleList</dt>
<dd>character list of gene names</dd>


<dt>GOGOA3</dt>
<dd>return value of subsetGOGOA()</dd>


<dt>ontology</dt>
<dd>character string c("molecular_function", "cellular_component", "biological_process")</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>


<dt>nrand</dt>
<dd>numeric number of randomizations to compute FDR</dd>


<dt>mn</dt>
<dd>integer param passed to trimGOGOA3, min size threshold for a category</dd>


<dt>mx</dt>
<dd>integer param passed to trimGOGOA3, max size threshold for a category</dd>


<dt>verbose</dt>
<dd>integer vector representing classes</dd>

</dl>

runGoMinerExamples: runGoMinerExamples

Description

Usage

Value

Arguments