Create network from edges statistical tests

network_from_tests(links, fdr)

Arguments

links: dataframe of the network edges and associated pvalues, as in the links attribute of the test_edges() method result.
fdr: threshold value such as all edges with adjusted pvalues lesser than the argument are be discarded for the final network construction

Value

Oriented weighted network as an igraph object

Examples

if (FALSE) {
data("abiotic_stresses")
data("gene_annotations")
data("regulators_per_organism")

genes <- get_locus(abiotic_stresses$heat_DEGs)
regressors <- intersect(genes, 
                        regulators_per_organism$`Arabidopsis thaliana`)

data <- aggregate_splice_variants(abiotic_stresses$normalized_counts)

r <- DIANE::group_regressors(data, genes, regressors)

mat <- DIANE::network_inference(r$counts, 
                                conds = abiotic_stresses$conditions, 
                                targets = r$grouped_genes,
                                regressors = r$grouped_regressors, 
                                importance_metric = "MSEincrease_oob", 
                                verbose = TRUE) 
res <- DIANE::test_edges(mat, normalized_counts = r$counts, density = 0.02,
                        nGenes = length(r$grouped_genes), 
                        nRegulators = length(r$grouped_regressors), 
                        nTrees = 1000, verbose = TRUE)
net <- DIANE::network_from_tests(res$links, fdr = 0.01)
}