Detect communities in a PPI network using the Louvain algorithm — louvain_cluster • unitcm

Applies the Louvain community detection algorithm to partition the PPI network into modules of densely connected genes.

Usage

louvain_cluster(graph, resolution = 1)

Arguments

graph: An igraph object (from build_ppi_network()).
resolution: Resolution parameter for the Louvain algorithm. Larger values produce more, smaller communities. Default 1.0.

Value

A named list where each element is a character vector of gene symbols belonging to one community. Community IDs are used as names.

Examples

if (FALSE) { # \dontrun{
ppi <- query_string_ppi(c("TP53", "BRCA1", "EGFR", "VEGFA", "TNF",
                           "MYC", "AKT1", "IL6", "JUN", "MAPK3"))
g <- build_ppi_network(ppi, unique(c(ppi$gene1, ppi$gene2)))
clusters <- louvain_cluster(g)
lengths(clusters)
} # }