Thanks Martin. I do have DO.db installed, and from the R shell I can type:

> getAnnMap("CHILDREN", "DO")
CHILDREN map for DO (object of class "AnnDbBimap")

However, it was complaining about an environment.

> showMethods("mget")
Function: mget (package base)
x="ANY", envir="AnnDbBimap"
x="ANY", envir="ANY"
x="character", envir="DOTermsAnnDbBimap"
    (inherited from: x="ANY", envir="AnnDbBimap")
x="character", envir="GOTermsAnnDbBimap"
    (inherited from: x="ANY", envir="AnnDbBimap")
x="character", envir="ProbeAnnDbBimap"
    (inherited from: x="ANY", envir="AnnDbBimap")
x="character", envir="ProbeGo3AnnDbBimap"
    (inherited from: x="ANY", envir="AnnDbBimap")

So, there's a version of mget that uses the environment "DOTermsAnnDbBimap".
I am guessing that this is the environment that it can't find.

Thanks for the hint - I'll track down and read that vignette. In the mean
time, I'm writing code to do the lookup I need as a special case.

Matthew

On 7 March 2011 01:47, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 03/06/2011 09:34 AM, Matthew Pocock wrote:
>
> > 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
> >
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>



-- 
Matthew Pocock
mailto: turingatemyhamster@gmail.com
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