[BioC] GO terms

[Marc Carlson]

Hi Heidi,

Looks like you have a lot of good tips already!

I will only add that if your terms are in a list you can also just
unlist() them 1st.  Like this:

Term(unlist(yourList))



  Marc



James W. MacDonald wrote:
>
>
> 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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>