Build a PPI network as an igraph object

Creates an igraph::graph() from STRING PPI edges. All genes in the input list are included as nodes (even those without interactions, as singletons). Edge weights are set to the STRING combined score divided by 1000 (i.e. in [0, 1]).

Usage

build_ppi_network(ppi_df, gene_list)

Arguments

ppi_df

A data frame from query_string_ppi() with columns gene1, gene2, score.

gene_list

Character vector of all gene symbols (used to ensure isolated nodes are included).

Value

An undirected igraph object with edge attribute weight.

Examples

if (FALSE) { # \dontrun{
ppi <- query_string_ppi(c("TP53", "BRCA1", "EGFR"))
g <- build_ppi_network(ppi, c("TP53", "BRCA1", "EGFR"))
igraph::vcount(g)
igraph::ecount(g)
} # }