[BioC] problem with getGOOntology
scory at mcb.mcgill.ca
Fri Apr 8 00:20:52 CEST 2005
> On Apr 7, 2005, at 5:20 PM, Sean Cory wrote:
>> I have two problems with the function getGOontology in package GOstats
>> (version 1.1.2)
>> 1) the environment GOTERM is not up date, this is a valid GO term (ION
>> BINDING) which does not appear.
>>> mget('GO:0043167', env = GOTERM, ifnotfound = NA)
>>  NA
> What version of GO? In version 1.7.0, it looks like it is defined....
> Can you send output of sessionInfo()?
Hi, I updated from 1.6.5 to 1.7.0 and it works.
> > mget('GO:0043167',env=GOTERM)
> GOID = GO:0043167
> Term = ion binding
> Definition = Interacting selectively with ions, charged atoms or small
> charged molecules.
> Ontology = MF
>> 2) the funcion getGOontology's documentation states that 'NA' will be
>> returned for incorrect terms, this is not the case. It returns an error
>> due to the last line in the function:
> I didn't find a function getGOontology. Can you post a little
> self-contained piece of code that mimics the problem?
>> return(sapply(wh, Ontology))
>> Doing the sapply on an 'NA' return an error
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