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

[Robert Gentleman]

Did anyone try

GOLeaves from the GOstats package? It seems to be documented to do what 
is wanted...


John Zhang wrote:
>> 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?).
> 
> That is right. GOBPOFFSPRING will give you all the children nodes but the node 
> structure is not preserved and there is no way to figure out which ones are the 
> outmost. 
> 
> You may need to travel through all the children nodes you get from the CHILDREN 
> environment to get down to the outmost leaf nodes.
> 
> 
>> many thanks
>>
>> John Zhang <jzhang at 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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> 
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
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206-667-7700
rgentlem at fhcrc.org