[BioC] GO terms

[James W. MacDonald]

Adrian Johnson wrote:
> Hi Heidi,
> Thanks for quick reply.
> It doesnt work for me. Although GOTERMS$"GO:ID" works.
> 
> I have all my GOIDs in a list, I want to get the terms for that IDs in
> character vector.

sapply(<GOID list>, function(x) Term(get(x, GOTERM)))

Best,

Jim


> 
> 
>> Term("GO:0006916")
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "Term", for
> signature "character"
> 
>> GOTERM$"GO:0006916"
> GOID: GO:0006916
> Term: anti-apoptosis
> Ontology: BP
> Definition: A process which directly inhibits any of the steps required
>     for cell death by apoptosis.
> Synonym: apoptosis inhibitor activity
> 
> Using GOTERM, I dont know how to capture 'Term'. I cannot use a sapply
> function over GOTERMS too.
> 
> -Adrian
> 
> 
> 
> 
> 
> 
> On Mon, Feb 15, 2010 at 6:53 PM, Heidi Dvinge <heidi at ebi.ac.uk> wrote:
>> Hello Adrian,
>>
>> if you just want the term and nothing else you can say e.g.
>>
>>> library(GO.db)
>> Loading required package: AnnotationDbi
>> Loading required package: Biobase
>>
>> Welcome to Bioconductor
>>
>>  Vignettes contain introductory material. To view, type
>>  'openVignette()'. To cite Bioconductor, see
>>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>>
>> Loading required package: DBI
>>> Term("GO:0006916")
>>      GO:0006916
>> "anti-apoptosis"
>>
>>
>> HTH
>> \Heidi
>>> Dear Group,
>>> Is there any function in GOstats or other packages,  that could give
>>> term name given GO ID.
>>>
>>> I have the result from probeSetSummary. I want to pull the GO term
>>> name along with GO term ID.
>>>
>>> Thanks
>>> Adrian
>>>
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>>
>>
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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