[BioC] problem with getGOOntology

Sean Davis sdavis2 at mail.nih.gov
Thu Apr 7 23:37:20 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)
> $"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()?

 > 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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