[BioC] problem with getGOOntology
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)
>  NA
What version of GO? In version 1.7.0, it looks like it is defined....
Can you send output of sessionInfo()?
GOID = GO:0043167
Term = ion binding
Definition = Interacting selectively with ions, charged atoms or small
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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