Functions for reading ontologies into R as lists and manipulating sets of ontological terms.
|Author||Daniel Greene <firstname.lastname@example.org>|
|Date of publication||2016-11-24 00:17:34|
|Maintainer||Daniel Greene <email@example.com>|
|License||GPL (>= 2)|
check: Perform simple consistency checks on 'ontology_index' object
exclude_descendants: Exclude terms descending from any in a given set of root...
get_ancestors: Get set of terms containing all ancestors of terms in a given...
get_descendants: Get set of terms containing all descendants of terms in a...
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...
minimal_set: Remove redundant/implied terms from a set of terms
mpo: MPO index
ontology_index: Create 'ontology_index' object from vectors and lists of term...
ontologyIndex-package: Functions for Reading Ontologies into R
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...