getGenes

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

getGenes function

<dl><dt>gs</dt>
<dd>gene set IDs; if NULL, returns all genes from all gene sets</dd>
<dt>genes</dt>
<dd>character vector with gene IDs. If not NULL, only genes
from this parameter will be considered.</dd>
<dt>fg</dt>
<dd>genes which are in the foreground set</dd>
<dt>mset</dt>
<dd>gene set to use (default: all tmod gene sets)</dd>
<dt>as.list</dt>
<dd>should a list of genes rather than a data frame be returned</dd></dl>

Arguments

Get genes belonging to a gene set — getGenes

<dl>

<dt>gs</dt>
<dd>gene set IDs; if NULL, returns all genes from all gene sets</dd>


<dt>genes</dt>
<dd>character vector with gene IDs. If not NULL, only genes
from this parameter will be considered.</dd>


<dt>fg</dt>
<dd>genes which are in the foreground set</dd>


<dt>mset</dt>
<dd>gene set to use (default: all tmod gene sets)</dd>


<dt>as.list</dt>
<dd>should a list of genes rather than a data frame be returned</dd>

</dl>

getGenes: Get genes belonging to a gene set

Description

Usage

Value

Arguments

Details