integrate_networks: Combine two (or more?) gene lists into a single integrated...

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

Combine two (or more?) gene lists into a single integrated network

Description

Combine two (or more?) gene lists into a single integrated network

Usage

integrate_networks(df_list, col, order, ppi_data = innatedb_exp, seed = 1)

Arguments

df_list	List of data frames; data to be integrated into a single network. If the list items do not have names, they will be assigned names using LETTERS.
col	Column containing Ensembl gene IDs; must be present in all elements of df_list.
order	Desired type of output network ("zero", "first", "min_simple" or "min_steiner"); passed to build_network()
ppi_data	Data frame of PPI data; must contain rows of interactions as pairs of Ensembl gene IDs, with columns named "ensembl_gene_A" and "ensembl_gene_B". Defaults to pre-packaged InnateDB PPI data.
seed	Number used in call to set.seed() to allow for reproducible network generation

Details

The "min_steiner" method is implemented with the SteinerNet package.

Value

tidygraph object for plotting or further analysis

References

See https://cran.r-project.org/web/packages/SteinerNet/index.html for details on the Steiner network trimming.

See Also

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

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