Given a collection of gene sets, the original network, and a set of permuted networks, calculates the empirical p-value using the direct interactions statistic (or average pairwise distance statistic).
For details on the tests performed on collections of gene sets (with examples), see direct_interactions_test() (or avg_pair_dist_test()).
| 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.
- distance (bool) – Flag whether to use average pairwise distance as the test statistic.
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- Returns:
- test_name (string) - name of test (either “Direct_Interactions_Statistic” or “Average_Pairwise_Distance_Ratio”).
- statistic (float) - test statistic of the collection on the original network
- pval (float) - empirical p-value of the collection on the original versus permuted networks.
- gene_set_results (list) - evaluation of each gene set using the original and permuted networks (see eval_gene_sets_by_interactions() and eval_gene_sets_by_dist() for details).
See also: direct_interactions_test(), avg_pair_dist_test().
