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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.
Health stats visible at Monitor.