overlap_community {CEMiTool}R Documentation

Generates communities from edgelist

Description

Returns communities from edgelist created by cemoverlap function.

Usage

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"))

Arguments

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 igraph package clustering function. One of 'cluster_fast_greedy', 'cluster_edge_betweenness', 'cluster_fast_greedy', 'cluster_label_prop', 'cluster_leading_eigen', 'cluster_louvain', 'cluster_optimal', 'cluster_spinglass' or 'cluster_walktrap'. Default: 'cluster_fast_greedy'

Details

Function takes edgelist as inputs and generates communities using functions provided in igraph package (default:'cluster_fast_greedy')

Value

A list containing the genes present in each community detected

Examples

## 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)

[Package CEMiTool version 1.6.11 Index]