## 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_obo()

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.