overlap_community {CEMiTool} | R Documentation |
Returns communities from edgelist created by cemoverlap function.
overlap_community(mod_intersection_df, presence_as_weights = FALSE, smallest_community = 15, method = c("cluster_fast_greedy", "cluster_edge_betweenness", "cluster_label_prop", "cluster_leading_eigen", "cluster_louvain", "cluster_optimal", "cluster_spinglass", "cluster_walktrap"))
mod_intersection_df |
Module intersection dataframe obtained from cemoverlap function |
presence_as_weights |
Logical. Should sums of node pair occurence be considered edge weights? |
smallest_community |
Minimal number of genes in community (default:15) |
method |
Character string denoting an |
Function takes edgelist as inputs and generates communities using functions provided in igraph package (default:'cluster_fast_greedy')
A list containing the genes present in each community detected
## Not run: # Run the cemitool function twice on expr dataset. Each time, one sample will be removed data(expr0) set.seed(10) dset1 <- expr0[,-sample(1:ncol(expr0), 1)] dset2 <- expr0[,-sample(1:ncol(expr0), 1)] cem1 <- cemitool(dset1, plot=FALSE) cem2 <- cemitool(dset2, plot=FALSE) cem_overlap_df <- cem_overlap(list(cem1, cem2)) comm_overlap_df <- overlap_community(cem_overlap_df) ## End(Not run)