Construct Meta Reciprocal Best Hits based on overlaps — construct_rbh_overlap

Iterate through a list containing membership matrices and construct pairwise networks for every combination, and output them as a symmetric matrix with labeled dimensions. This can be interpreted as an "adjacency" matrix between all of the different metagenes across networks in the input list. The column/row names will take each networks communities' names and concatenate them with the network list names, such that the dimension names are guaranteed to be unique.

Usage

construct_rbh_overlap_based(network_membership_list, top_n = 50, memb_cut = 0)

Arguments

network_membership_list: a list containing community membership scores for each network. Where rownames contain unique gene ids and column names are community names
top_n: the number of top genes based on membership scores with higher scores indicating stronger membership in a community
memb_cut: membership threshold for stricter thresholding. Only genes with membership score greater the threshold are used

Examples

if (FALSE) {
memb_list <- list(
  GSE39582 = GSE39582_icwgcna$community_membership,
  READ = read_icwgcna$community_membership,
  COAD = coad_icwgcna$community_membership
)
ma <- construct_rbh_overlap_based(memb_list)
}