[BioC] how to extract GO terms at different level of DAG

[Marc Carlson]

Hi Ed,

You didn't follow the posting guide and give me an example to work with 
so I have to make one up.  So here goes.  Lets suppose that you had this 
GO term you were interested in: GO:0000127 "transcription factor TFIIIC 
complex", I also note that this term is a CC term. That detail will be 
important below.  You can learn all this from the GOTERM mapping in the 
GO.db package BTW like this:

library(GO.db)
Term("GO:0000127")
Ontology("GO:0000127")

Now lets suppose that we wanted to know who the parent and child terms 
are for this GO ID.  How would we do it?  Like this:

get("GO:0000127", GOCCPARENTS)

get("GO:0000127", GOCCCHILDREN)

And what if we wanted to know all the parents or all the children all 
the way up/down the DAG? Like this:

get("GO:0000127", GOCCANCESTOR)

get("GO:0000127", GOCCOFFSPRING)


Hope this helps,


   Marc





On 07/14/2011 09:17 AM, Ed wrote:
> I would like to rephrase my question like,
>
> If I have a horizontal "cut" across the hierarchical structure of GO term at
> the level of 5, for example, could I know their parent-child relationship
> for the GO terms?
>
> Thanks,
>
> Ed
>
> On Thu, Jul 14, 2011 at 11:00 AM, Ed<edforum at gmail.com>  wrote:
>
>> Hi there,
>>
>> I searched the archive and did not find the answer so I posted here and
>> hope to get some suggestion..
>>
>> I intend to extract GO terms at different level of GO's DAG; for example, I
>> would like to know within BP, at the level of 3 to 5, what those GO terms
>> are and what entrezgene ids are associated with each term.
>>
>> Thanks,
>>
>> Ed
>>
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