modGroups

Find group of modules based on shared genes

Methods and feature set definitions for feature or gene set
enrichment analysis in transcriptional and metabolic profiling data.
Package includes tests for enrichment based on ranked lists of features,
functions for visualisation and multivariate functional analysis. See Zyla et al (2019)
<doi:10.1093/bioinformatics/btz447>.

January Weiner

tmod

Feature Set Enrichment Analysis for Metabolomics and
Transcriptomics

modGroups function

<dl><dt>modules</dt>
<dd>Either a list of modules or character vector.</dd>
<dt>mset</dt>
<dd>Which module set to use. Either a character vector ("LI", "DC" or "all", default: all) or an object of class tmod (see "Custom module definitions" below)</dd>
<dt>min.overlap</dt>
<dd>Minimum number of overlapping items if stat ==
number, minimum jaccard index if stat == jaccard etc.</dd>
<dt>stat</dt>
<dd>Type of statistics to return. 
"jaccard": Jaccard index (default);
"number": number of common genes;
"soerensen": Soerensen-Dice coefficient;
"overlap": Szymkiewicz-Simpson coefficient.</dd></dl>

Arguments

Find group of modules — modGroups

<dl>

<dt>modules</dt>
<dd>Either a list of modules or character vector.</dd>


<dt>mset</dt>
<dd>Which module set to use. Either a character vector ("LI", "DC" or "all", default: all) or an object of class tmod (see "Custom module definitions" below)</dd>


<dt>min.overlap</dt>
<dd>Minimum number of overlapping items if stat ==
number, minimum jaccard index if stat == jaccard etc.</dd>


<dt>stat</dt>
<dd>Type of statistics to return. 
"jaccard": Jaccard index (default);
"number": number of common genes;
"soerensen": Soerensen-Dice coefficient;
"overlap": Szymkiewicz-Simpson coefficient.</dd>

</dl>

modGroups: Find group of modules

Description

Usage

Arguments

Details

Examples