module_networks {pGRN}

Get module level networks

Description

Given a distance matrix, calculate gene modules based on hierarchical clustering method and then get module level networks

Usage

module_networks(
  data,
  k = 10,
  quantile_cutoff = 10,
  centrality_degree_mod = "out",
  components_mod = "weak",
  network_min_genes = 10
)

Arguments

data

distance matrix

k

number of gene clusters for module inference

quantile_cutoff

distance cutoff based on quantile(1-99) for edge identification

centrality_degree_mod

"in" or "out" for nodes popularity calculation

components_mod

"weak" or "strong" for sub-network components inference

network_min_genes

minial number of genes required for a network

Value

a list networks for each module

Examples

example_data <- pGRNDB
expression_matrix <- example_data[["expression"]]
pseudotime_list <- example_data[["ptime"]]$PseudoTime
dtw_dist_matrix <- get_dtw_dist_mat(expression_matrix,
                                    pseudotime_list,
                                    cores=1)
nets <- module_networks(dtw_dist_matrix,k=1,quantile_cutoff=50)
plot_network(nets[["module1"]])