multi_dendrix.evaluate.network.eval_gene_sets_by_interactions

multi_dendrix.evaluate.network.eval_gene_sets_by_interactions(collection, G, Hs)

Evaluate each of the t individual gene sets by comparing the number of interactions within a gene set in the original PPI network G to the permuted networks Hs.

Parameters:

• collection (list of lists) – collection of gene sets to be tested.
• G (NetworkX Graph.) – original PPI network.
• Hs (list of NetworkX Graphs) – permuted versions of G.

Returns:

A list of t tuples where each tuple contains:

• gset (list) - the original gene set.
• num_interactions (int) - the number of interactions among genes set in the original network.
• pval (float) - the empirical p-value of the gene set’s test statistic (i.e. the number of interactions) in the permuted networks.

See also: evaluate_collection(), eval_gene_sets_by_dist(), direct_interactions_test().