save_gnet: Save the GNET2 results

In chrischen1/GNET2: Constructing gene regulatory networks from expression data through functional module inference

Save the GNET2 results

Description

Save the edge list, group index of each gene and plot the top groups

Usage

save_gnet(gnet_result, save_path = ".", num_module = 10, max_gene_num = 100)

Arguments

gnet_result	Results returned by gnet().
save_path	path to save files
num_module	The number of modules with highest score to plot.
max_gene_num	The max number of genes to show in the heatmap.

Value

None

Examples

set.seed(1)
init_group_num = 5
init_method = 'boosting'
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)
save_gnet(gnet_result)

chrischen1/GNET2 documentation built on June 29, 2022, 8:53 a.m.