Hi John,

Thanks for the reply. I tried the following:

t("GO:0008150", GOBPCHILDREN)
> length(g1)
[1] 12
> g1
 [1] "GO:0050789" "GO:0050896" "GO:0009987" "GO:0016032"
 [5] "GO:0043473" "GO:0019952" "GO:0000003" "GO:0000004"
 [9] "GO:0040007" "GO:0007275" "GO:0007582" "GO:0051704"


So, starting with the root node for biological process, I would want to get only the outermost leaf nodes (and not any intermediate nodes in the graph). 

The above code would appear to give the direct children of the root node (is that correct?).

many thanks

John Zhang <jzhang@jimmy.harvard.edu> wrote: 
>
>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?

Just for the GO ids:

>library(GO)
>leafGOs <- get("GO:0003674", GOMFCHILDREN)



>
>thanks!
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084



       
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