extract_edges: Extract the network from the gnet result

In jianlin-cheng/GNET2: Constructing gene regulatory networks from expression data through functional module inference

Description

Extract the network as edge list from the gnet result. For a module, each regulator and downstream gene will form a directed edge.

Usage

extract_edges(gnet_result)

Arguments

gnet_result

Returned results from gnet().

Value

A matrix of scores of for the regulator-target interaction.

Examples

set.seed(1)
init_group_num = 8
init_method = 'kmeans'
exp_data <- matrix(rnorm(50*10),50,10)
reg_names <- paste0('TF',1:5)
rownames(exp_data) <- c(reg_names,paste0('gene',1:(nrow(exp_data)-length(reg_names))))
colnames(exp_data) <- paste0('condition_',1:ncol(exp_data))
se <- SummarizedExperiment::SummarizedExperiment(assays=list(counts=exp_data))
gnet_result <- gnet(se,reg_names,init_method,init_group_num)
edge_list <- extract_edges(gnet_result)

jianlin-cheng/GNET2 documentation built on Oct. 22, 2020, 11:24 p.m.