lookUp for other terminologies
1
0
Entering edit mode
@matthew-pocock-4529
Last seen 9.6 years ago
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]]
Annotation GO Annotation GO • 819 views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 6 weeks ago
United States
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
ADD COMMENT
0
Entering edit mode
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]]
ADD REPLY
0
Entering edit mode
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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLY

Login before adding your answer.

Traffic: 768 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6