Function reference • Higana

Ontology
`annotate()`	Annotate ontology with gene annotations.
`collapse_redundant_terms()`	Collapse terms whose annotations are redundant with respect to their children.
`collapse_terms()`	Collapse a set of terms, rerouting their children directly to their parents.
`compute_redundancy()`	Compute redundancy score for each term.
`filter()`	Filter ontology to a specific set of terms.
`filter_obsolete()`	Removes obsolete terms from the ontology.
`filter_unannotated()`	Removes unannotated terms from the ontology.
`permute()`	Permute an ontology.
`propagate_annotations()`	Propagates annotations up through the hierarchy.
`read_bed()`	Open PLINK .bed file and create gene mapping.
`read_gaf()`	Read annotations from GAF file.
`read_obo()`	Read ontology from OBO file.
`recompute_ancestors()`	Recomputes `ancestors` field for each term.
`unite_roots()`	Unites a set of roots in the ontology under a common root.
Dimensionality reduction
`compute_gene_pcs()`	Compute principal components of SNPs annotated to genes.
`compute_term_pcs()`	Compute principal components of SNPs annotated to ontology terms.
`compute_term_pcs_stepdown()`	Compute principal components of ontology terms for stepdown test.
`extract_pcs()`	Extract the PCs of a specific set of terms.
Association analysis
`test_genes()`	Perform association test for genes.
`test_terms()`	Perform association test for terms.
Visualization
`plot_hierarchy()`	Plot part of an ontology as a tree.

Reference