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. |