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.
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
--
Matthew Pocock
mailto: turingatemyhamster@gmail.com
gchat: turingatemyhamster@gmail.com
msn: matthew_pocock@yahoo.co.uk
irc.freenode.net: drdozer
(0191) 2566550
[[alternative HTML version deleted]]
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
>
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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
gchat: turingatemyhamster@gmail.com
msn: matthew_pocock@yahoo.co.uk
irc.freenode.net: drdozer
(0191) 2566550
[[alternative HTML version deleted]]
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
> gchat: turingatemyhamster at gmail.com
> msn: matthew_pocock at yahoo.co.uk
> irc.freenode.net: drdozer
> (0191) 2566550
>
> ? ? ? ?[[alternative HTML version deleted]]
>
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