[BioC] lookUp for other terminologies

[Vincent Carey]

I am going to move this thread to bioc-devel and comment further there.

On Mon, Mar 7, 2011 at 3:55 AM, Matthew Pocock
<turingatemyhamster at gmail.com> wrote:
> 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 at 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 at gmail.com
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>
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