pGRN (version 0.3.5)

get_networks: Get the list of sub-networks

Description

Get sub-networks based on given adjacency data.frame input

Usage

get_networks(
  data,
  centrality_degree_mod = "out",
  components_mod = "weak",
  network_min_genes = 10
)

Value

list of tabl_graph objects

Arguments

data

adjacency data.frame

centrality_degree_mod

mode of centrality degree for popularity calculation

components_mod

mode of sub-network extraction methods

network_min_genes

minimal number of gene elements required for extracted sub-networks

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)
adj_df <- matrix2adj(dtw_dist_matrix)
get_networks(adj_df,network_min_genes=5)