ontologyIndex-package | Functions for Reading Ontologies into R |
exclude_branches | Exclude terms descending from particular term from a character vector of terms |
force_compatibility | Remove alternate/deprecated term IDs and swap for new ones |
get_ancestors | Get set of all ancestors of set of terms |
get_descendants | Get set of all descendants of single term |
get_mpo_to_hpo | Get MPO to HPO list |
get_ontology | Get R-Object representation of ontology from obo file |
get_terms_by_set_matrix | Get a matrix with columns of hpo terms and rows of patients, |
get_term_ancestors | Get property of individual ontological term |
get_term_children | Get property of individual ontological term |
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_names | Get property of individual ontological term |
get_term_parents | Get property of individual ontological term |
get_term_property | Get property of individual ontological term |
go | GO index |
hpo | HPO index |
intersection_with_branches | Intersect set of terms with branches of ontology |
minimal_set | Remove redundant/implied terms |
mpo | MPO index |
mpo_to_hpo | Mapping from MPO to HPO |
ontologyIndex | Functions for Reading Ontologies into R |
prune_branches | Prune all terms descending from given term down to that term and ensure no degeneracy |