Detect Communities in Adjacency/Reciprocal Best Hits Matrix

Performs Markov Clustering on the adjacency matrix, giving the cluster/community number that each metagene is associated with, renamed so that the clusters are in order of size (1 being the largest)

Usage

detect_consensus_communities(rbh, expansion = 2)

Arguments

rbh

adjacency/reciprocal best hits matrix, as output by construct_rbh_correlation_based()

expansion

numeric value > 1 for the expansion parameter

Value

The output of MCL::mcl(), renamed so that the clusters are in order of size (1 being the largest)

Details

See MCL::mcl() for more detail

Examples

if (FALSE) {
# Create list of community_membership object
memb_list <- list(
  GSE39582 = GSE39582_icwgcna$community_membership,
  READ = read_icwgcna$community_membership,
  COAD = coad_icwgcna$community_membership
)
ma <- construct_rbh_correlation_based(
  memb_list,
  upper_quant = .99,
  lower_quant = .05,
  max_rank = 2
)
consensus_comms <- detect_consensus_communities(ma)
}