combine_overlapping_pathways

Modify a pathway list to combine overlapping pathways.

internal

Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) <doi:10.1038/s41598-019-41918-3>. Provides summary functions to break down the results at the pathway, gene, or individual connection level. The differential networks for each pathway of interest can be plotted, and the visualization will highlight any differentially expressed genes and all of the gene-gene associations that are significantly differentially connected.

Tyler Grimes

dnapath

Differential Network Analysis using Gene Pathways

Somnath Datta

combine_overlapping_pathways function

<dl><dt>pathway_list</dt>
<dd>A list of pathways obtained from
<code>get_reactome_pathways</code>.</dd>
<dt>overlap_limit</dt>
<dd>A percentage between 0 and 1. If two pathways
overlap by more than this amount, they are combined into one pathway.</dd></dl>

Arguments

Modify a pathway list to combine overlapping pathways. — combine_overlapping_pathways

<dl>

<dt>pathway_list</dt>
<dd>A list of pathways obtained from
<code>get_reactome_pathways</code>.</dd>


<dt>overlap_limit</dt>
<dd>A percentage between 0 and 1. If two pathways
overlap by more than this amount, they are combined into one pathway.</dd>

</dl>

combine_overlapping_pathways: Modify a pathway list to combine overlapping pathways.

Description

Usage

Value

Arguments