extract_subnetwork: Extract a subnetwork based on pathway genes

In travis-m-blimkie/networker: Reproducible PPI Network Creation and Visualization in R

Extract a subnetwork based on pathway genes

Description

Extract a subnetwork based on pathway genes

Usage

extract_subnetwork(network, genes = NULL, enrich_result = NULL, pathway_name)

Arguments

network	Input network object; output from build_network
genes	List of Ensembl gene IDs to use as the starting point to extract a subnetwork from the initial network. You must provide either genes or enrich_result argument.
enrich_result	Pathway enrichment result, output from enrich_network. You must provide either genes or enrich_result argument.
pathway_name	Name of the pathway determining what genes (nodes) are pulled from the input network.

Details

Uses functions from the igraph package to extract a minimally connected subnetwork or module from the starting network, using either a list of Ensembl genes or genes from an enriched pathway as the basis. To see what genes were pulled out for the pathway, check attr(x, "starters").

Value

tidygraph object for plotting or further analysis

References

Code for network module (subnetwork) extraction was based off of that used in jboktor/NetworkAnalystR on Github.

See Also

https://www.github.com/travis-m-blimkie/networker

travis-m-blimkie/networker documentation built on June 3, 2023, 10:17 p.m.