get_networks: Get the list of sub-networks

In pGRN: Single-Cell RNA Sequencing Pseudo-Time Based Gene Regulatory Network Inference

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
)

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

Value

list of tabl_graph objects

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)

pGRN documentation built on Jan. 18, 2023, 1:06 a.m.