# Reading Ontologies into R

## Documentation for package ‘ontologyIndex’ version 2.12

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

ontologyIndex-package | Functions for Reading Ontologies into R
as.data.frame.ontology_index | Case 'ontology_index' object to 'data.frame'
check | Check an 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_OBO | Read ontology from OBO file into R
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 | 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.