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get_ontology now has option merge_equivalent_terms (TRUE by default) so that terms that are marked equivalent_to other terms are merged and properties aggregated (thanks to feedback from Vincent Carey).get_ancestors now returns an empty character vector rather than NULL when terms argument is empty.*_branches functions have all been renamed to *_descendants and their branch_roots argument to roots.get_descendants function has had two arguments renamed: ancestor is now roots and can accept a vector of root terms, returning the set of all terms which descend from them; remove_ancestor is now exclude_roots, determining whether or not to exclude the given roots terms from the result.check function which checks whether an ontology is valid has been added.ontology_indexes.print has been added for ontology_indexes.get_ontology now only requires a file argument.ontology_index objects now contain an obsolete slot - a logical vector.prune_branches, exclude_branches and intersection_with_branches now use the same signature and are renamed to reflect the possibilit of passing multiple branch roots.get_term_property, get_term_parents, get_term_ancestors and get_term_children functions with as_names argument to get descriptive names added for convenience.swap_out_alt_ids replaced with force_compatibility which optionally throws an error if non-matchable term IDs are passed.data(go) now loads an ontology_index of the Gene Ontology (2015-11-27).These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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