detect_communities: Detect communities in a network

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

Detect communities in a network

Description

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.

Author(s)

Fabricio Almeida-Silva

See Also

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

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)

almeidasilvaf/BioNERO documentation built on March 25, 2024, 9:14 p.m.