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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_index
es.print
has been added for
ontology_index
es.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.