[BioC] Finding GO leaf nodes for an ontology - which package?

Herve Pages hpages at fhcrc.org
Fri Jul 27 20:08:21 CEST 2007

Hi Tim,

Have you tried this?

> library(GO)
> isleaf <- unlist(eapply(GOBPCHILDREN, function(goid) isTRUE(is.na(goid))))

Now isleaf is a logical vector whose names are all the BP goids: for each BP goid
it tells whether it is a leaf or not.

To put the BP leaves in a character vector:

> BPleaves <- names(isleaf)[isleaf]


Tim Smith wrote:
> Hi,
> I was trying to list all the leaf nodes for a particular ontology. For this, I was using the GOstats:
> g1 <- oneGOGraph("GO:0003674", GOMFCHILDREN)
> g2 <- GOleaves(g1)
> Hopefully, this would give me a list of all the leaf nodes for the molecular function ontology. But this is taking too long to execute.
> Is there a similar function in some other package that would be quicker?
> thanks!
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