check                   Perform simple consistency checks on
                        'ontology_index' object
exclude_descendants     Exclude terms descending from any in a given
                        set of root terms
get_ancestors           Get set of terms containing all ancestors of
                        terms in a given set
get_descendants         Get set of terms containing all descendants of
                        terms in a given set
get_ontology            Read ontology from OBO file into R
get_relation_names      Get names of relations used in OBO file
get_term_descendancy_matrix
                        Get logical descendancy matrix for set of terms
get_term_frequencies    Get frequency of each term in a set of
                        phenotypes
get_term_info_content   Get information content of each term in a set
                        of phenotypes
get_term_property       Get property of individual ontological term
go                      GO index
hpo                     HPO index
intersection_with_descendants
                        Intersect a set of terms with the descendants
                        of a given set of roots
minimal_set             Remove redundant/implied terms from a set of
                        terms
mpo                     MPO index
ontologyIndex-package   Functions for Reading Ontologies into R
ontology_index          Create 'ontology_index' object from vectors and
                        lists of term properties
print.ontology_index    Print 'ontology_index' object.
propagate_relations     Select terms by propagating relations from a
                        set of terms
prune_descendants       Exclude terms descending from a given set of
                        roots but include those roots which were
                        originally implicitly present.
