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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.
Health stats visible at Monitor.