Function hpo::stats::hypergeom::gene_enrichment

pub fn gene_enrichment<'a, T, U>(
    background: T,
    set: U
) -> Vec<Enrichment<GeneId>>
where
    T: IntoIterator<Item = HpoTerm<'a>>,
    U: IntoIterator<Item = HpoTerm<'a>>,

Calculates the hypergeometric enrichment of genes within the set compared to the background

Examples

use hpo::Ontology;
use hpo::{HpoSet, term::HpoGroup};
use hpo::stats::hypergeom::gene_enrichment;

let ontology = Ontology::from_binary("tests/example.hpo").unwrap();

let gene = ontology.gene_by_name("EZH2").unwrap();
let gene_hpo_set = gene.to_hpo_set(&ontology);

let mut enrichments = gene_enrichment(&ontology, &gene_hpo_set);

// the results are not sorted by default
enrichments.sort_by(|a, b| {
        a.pvalue().partial_cmp(&b.pvalue()).unwrap()
});
assert!(enrichments.first().unwrap().pvalue() < enrichments.last().unwrap().pvalue());
assert!(enrichments.first().unwrap().enrichment() > enrichments.last().unwrap().enrichment());