Module hpo::stats::hypergeom

Calculate the enrichment of a gene or disease in an HpoSet and the probability of enrichment within the hypergeometric distribution.

These methods are useful when you have clinical information of a patient and want to see if the terms are enriched for some genes or diseases.

Examples

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

fn clinial_info_set(ontology: &Ontology) -> HpoSet {
// ...
}

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

let patient_ci = clinial_info_set(&ontology);
let mut enrichments = gene_enrichment(&ontology, &patient_ci);
     
// the results are not sorted by default
enrichments.sort_unstable_by(|a, b| {
        a.pvalue().partial_cmp(&b.pvalue()).unwrap()
    });

for gene in enrichments {
    println!("{}\t{}\t({})", gene.id(), gene.pvalue(), gene.enrichment());
}

You can also use it to find genes that have a similar phenotype to a gene. Here we are creating an HpoSet from all crate::HpoTerms that are directly connected to the gene EZH2. We’re then checking which genes are enriched in the directly and indirectly linked HpoTerms.

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());

Functions

• disease_enrichment
  Calculates the hypergeometric enrichment of diseases within the set compared to the background
• gene_enrichment
  Calculates the hypergeometric enrichment of genes within the set compared to the background