Compute the average metagene across studies for each community

Usage

calc_consensus_memberships(
  consensus_comms,
  network_membership_list,
  weights = NULL,
  gene_cohort_N = 3,
  compressIntra = c("first", "mean"),
  remove_misc_comm = TRUE,
  comm_prefix = "mA"
)

Arguments

consensus_comms: communities output from MCL::mcl(), a list containing elements Cluster with a vector of the cluster associated with each index.
network_membership_list: a list containing community membership scores for each network. Where rownames contain unique gene ids and column names are community names
weights: weights for weighted average of based on study attributes
gene_cohort_N: number of studies a gene must be present in to be included
compressIntra: indicates how to deal with multiple metagenes belonging to the same community within one study-level network
remove_misc_comm: should the miscellaneous community be removed (1st community)
comm_prefix: the prefix to add to community names

Value

matrix with average loadings (metagenes) across studies included from network_membership_list

Examples

if (FALSE) {
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)
consensus_memb <- calc_consensus_memberships(consensus_comms, memb_list)
}