[BioC] lookUp for other terminologies

[Martin Morgan]

On 03/06/2011 09:34 AM, Matthew Pocock wrote:
> Hi,
> 
> I'm trying to use DO in stead of GO with some bioconductor functions. I've
> made a hu6800DO bimap that associates the chip IDs with DO IDs. Now I'm
> adapting existing code that calls lookUp(id, annotation, extension) and
> using annotation "hu6800" and extension "DO". This is failing with:
> 
> Error in mget(x, envir = getAnnMap(what, chip = data, load = load),
> ifnotfound = NA) :
>   error in evaluating the argument 'envir' in selecting a method for
> function 'mget'
>> traceback()
> 3: mget(x, envir = getAnnMap(what, chip = data, load = load), ifnotfound =
> NA)
> 2: lookUp(id, annotation, extension) at gtDO.R#144
> 
> So it looks like getAnnMap is not happy. I've looked at the source for
> getAnnMap and have to own up to being mystified by it.

Hi Matthew -- if I

  getAnnMap("CHILDREN", "DO")

then getAnnMap is going to look in search() for an entry that might look
like "package:DO.db" and then use that to find a map DOCHILDEN. If it
can't find the package in search(), it'll try to load it.

What this means, I think, is that you'd want to create not just a bimap
but a package that contains the bimap. I think this is covered in the
AnnotationDbi package vignette "SQLForge: ...easy...". Not sure this is
the most straight-forward path to your objective...

Martin


> 
> I think the closest 'drop-in' replacement I can find in DO for lookUp is the
> Term() function, but I may be confused about what these two different
> functions do.
> 
> Thanks,
> 
> Matthew
> 


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