Detect communities in a network

Detect communities in a network

Usage

detect_communities(edgelist, method = igraph::cluster_infomap, directed = TRUE)

Arguments

edgelist

Data frame containing the network as an edge list. First column must be node 1 and second column must be node 2. Additional columns will be interpreted as edge attributes and will be modified by this function.

method

igraph function to be used for community detection. Available functions are cluster_infomap, cluster_edge_betweenness, cluster_fast_greedy, cluster_walktrap, cluster_spinglass, cluster_leading_eigen, cluster_louvain, and cluster_label_prop. Default is cluster_infomap.

directed

Logical indicating whether the network is directed (GRN only) or not (GCN and PPI networks). Default: TRUE.

Value

A data frame containing node names in the first column, and communities to which nodes belong in the second column.

See also

cluster_infomap, cluster_edge_betweenness, cluster_fast_greedy, cluster_walktrap, cluster_spinglass, cluster_leading_eigen, cluster_louvain, cluster_label_prop

Author

Fabricio Almeida-Silva

Examples

data(filt.se)
tfs <- sample(rownames(filt.se), size=50, replace=FALSE)
grn_edges <- grn_infer(filt.se, method = "clr", regulators = tfs)
com <- detect_communities(grn_edges, directed=TRUE)