Functions for reading ontologies into R as lists and manipulating sets of ontological terms - 'ontologyX: A suite of R packages for working with ontological data', Greene et al 2017
*_branchesfunctions have all been renamed to
get_descendantsfunction has had two arguments renamed:
rootsand can accept a vector of root terms, returning the set of all terms which descend from them;
exclude_roots, determining whether or not to exclude the given
rootsterms from the result.
checkfunction which checks whether an ontology is valid has been added.
get_ontologynow only requires a
ontology_indexobjects now contain an
obsoleteslot - a
intersection_with_branchesnow use the same signature and are renamed to reflect the possibilit of passing multiple branch roots.
as_namesargument to get descriptive names added for convenience.
force_compatibilitywhich optionally throws an error if non-matchable term IDs are passed.
data(go)now loads an
ontology_indexof the Gene Ontology (2015-11-27).