[BioC] problem with getGOOntology

[Sean Cory]

>
> 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)
>> $"GO:0043167"
>> [1] 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.

thanks

Sean Cory

>
>  > mget('GO:0043167',env=GOTERM)
> $"GO:0043167"
> 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
>