tmodLEA

For each module, return a list of genes on the leading edge

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

tmodLEA function

<dl><dt>l</dt>
<dd>list of genes</dd>
<dt>modules</dt>
<dd>character vector of module IDs for which to run the LEA</dd>
<dt>mset</dt>
<dd>Which module set to use. Either a character vector ("LI", "DC" or "all", default: LI) or an object of class tmod</dd>
<dt>nodups</dt>
<dd>Remove duplicate gene names in l and corresponding
rows from ranks</dd>
<dt>filter</dt>
<dd>Remove gene names which have no module assignments</dd></dl>

Arguments

Leading Edge Analysis — tmodLEA

<dl>

<dt>l</dt>
<dd>list of genes</dd>


<dt>modules</dt>
<dd>character vector of module IDs for which to run the LEA</dd>


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


<dt>nodups</dt>
<dd>Remove duplicate gene names in l and corresponding
rows from ranks</dd>


<dt>filter</dt>
<dd>Remove gene names which have no module assignments</dd>

</dl>

tmodLEA: Leading Edge Analysis

Description

Usage

Arguments

Details