[BioC] problem with getGOOntology

[Francois Pepin]

Taking over from Sean (the original poster, who's sitting beside me) a
little bit.

The original problem was that some of the annotation packages referred
(mouse4302) to a GO term that wasn't in the GO package. As Sean Davis
correctly pointed out, it is in the version 1.7.0, while we had 1.6.5. I
thought that the GOTERM env was in GOstats (which was up to date), and I
wasn't aware of the GO package.

That part of the problem is now fixed, and as far as we're concerned, so
the code is working.

The problem was with GOHyperG, which uses getGOOntology to limit itself
to a given category of terms. In this particular case, the ordering is
crucial. Between changing the ordering and giving the error, I'd rather
have the error.

The reason we're calling this a bug is that the documentation says that
NA's would be produced:
(from the bottom of ?getGOOntology)
     For 'getGOOntology' a vector of categories (the names of which are
     the original GO term names). Elements of this list that are 'NA'
     indicate term names for which there is no category (and hence they
     are not really term names).

Ideally, NA's would be inserted. The next best solution would be to
change the documentation and say that an error would be produced if any
invalid term is inserted.

Francois

On Thu, 2005-04-07 at 18:17, Robert Gentleman wrote:
> Yes, it probably requires a slightly better handling of missing values  
> (although that is a bit of a can of worms). I will try to see what can  
> be done in time for the next release.
> 
> If you are interested you might try defining the following method -  
> largely untested as I am travelling -
> 
> setMethod("Ontology", signature="ANY", function(object) if(  
> is.na(object) ) NA else    callNextMethod())
> 
> with that in place I get:
>  > getGOOntology("GO:11111")
> GO:11111
>        NA
> 
> which seems like what is wanted, but I am sure there will be  
> consequences. Let me know if that triggers more downstream nastiness -  
> as I am not just sure of where you are going (note also we don't seem  
> to have either sessionInfo for the  original report nor a workable  
> example of what is wanted - these are kind of important)
> 
> On Apr 7, 2005, at 2:59 PM, Francois Pepin wrote:
> 
> > On Thu, 2005-04-07 at 17:58, Sean Davis wrote:
> >
> >>>> getGOOntology
> >>> function (x)
> >>> {
> >>>     if (!is.character(x))
> >>>         stop("need a character argument")
> >>>     if (length(x) == 0)
> >>>         return(character(0))
> >>>     wh <- mget(x, env = GOTERM, ifnotfound = NA)
> >>>     return(sapply(wh, Ontology))
> >>> }
> >>>
> >>
> >> My bad.  The lowercase 'o' got me.
> >>
> >> If you haven't already done it, looks like a line:
> >>
> >> wh <- wh[!is.na(wh)]
> >>
> >> right before the return line might do the trick.
> >
> > Not quite, as it would mess the indices up if you were to load a list  
> > of
> > terms.
> >
> > Instead of having c('MF', NA, NA, 'CC', 'BP') as a result you'd end up
> > having c('MA','CC','BP') and think that the 3rd one is a biological
> > process term rather than not being a GO term (and have no clue for the
> > last 2).
> >
> > Francois
> >
> >
> >> Sean
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
> >
> +----------------------------------------------------------------------- 
> ----------------+
> | Robert Gentleman              phone: (206) 667-7700                    
>           |
> | Head, Program in Computational Biology   fax:  (206) 667-1319   |
> | Division of Public Health Sciences       office: M2-B865               
>        |
> | Fred Hutchinson Cancer Research Center                                 
>           |
> | email: rgentlem at fhcrc.org                                              
>                           |
> +----------------------------------------------------------------------- 
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