[BioC] Annotation.db: how automatically call a mapping?

[Hooiveld, Guido]

Hi Perry,

Thanks for your suggestion. Compared to my efforts this is much more
generic, which I prefer. :)
I'll give it a try and let you know.

Guido
 

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> P.D. Moerland
> Sent: 29 June 2009 22:07
> To: Hooiveld, Guido
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Annotation.db: how automatically call a mapping?
> 
> Dear Guido,
> 
> A few weeks back I was struggling with the same problem and 
> came up with this solution:
> 
> 
> makeMapping <- function(annotPkg,str="SYMBOL",ids){
> 	do.call(library,list(annotPkg))
> 	annotPkg = sub(".db","",annotPkg)
> 	f = function(x) mget(ids,x,ifnotfound=NA)
> 	annot = do.call(f,list(get(paste(annotPkg,str,sep=""))))
>        return(annot)
> }
> 
> Just as an example:
> 
> > 
> makeMapping("moe430a.db",str="SYMBOL",ids=c("1415670_at","1415671_at")
> > )
> 
> $`1415670_at`
> [1] "Copg"
> 
> $`1415671_at`
> [1] "Atp6v0d1"
> 
> 
> best,
> Perry
> 
> ---
> Perry Moerland, PhD
> Room J1B-206, Bioinformatics Laboratory
> Department of Clinical Epidemiology, Biostatistics and 
> Bioinformatics Academic Medical Centre, University of 
> Amsterdam Postbus 22660, 1100 DD Amsterdam, The Netherlands
> tel: +31 20 5664660
> p.d.moerland at amc.uva.nl, http://www.amc.uva.nl/
> 
> ----- Original Message -----
> From: "Hooiveld, Guido" <Guido.Hooiveld at wur.nl>
> Date: Monday, June 29, 2009 9:43 pm
> Subject: [BioC] Annotation.db: how automatically call a mapping?
> To: bioconductor at stat.math.ethz.ch
> 
> 
> > Hi,
> >  
> > I am facing a problem i cannot solve myselves, despite everything i 
> > read/know. But i assume the solution is easy for the more 
> knowledgable 
> > folks in BioC/R...
> >  
> > This does work:
> > > library(moe430a.db)
> > > xxyy <- moe430aSYMBOL
> > > xxyy
> > SYMBOL map for chip moe430a (object of class "AnnDbBimap")
> >  
> > However, for this to work you need to know the array type 
> of the data 
> > that is analyzed.
> >  
> >  
> > Now i would like to automatically extract the (e.g.) SYMBOL mapping 
> > from an annotation.db, thus by retrieving the array type 
> from the eset.
> >  
> > > library(affy)
> > > eset <- rma(data)
> > > probeids <- featureNames(eset)
> > > annotation(eset)
> > [1] "moe430a"
> >  
> > But how can i use this info to properly call the SYMBOL mapping?
> >  
> > I tried this:
> > > arraytype <- annotation(eset)
> > > arraytype <- paste(arraytype, "db", sep = ".") arraytype
> > [1] "moe430a.db"
> > > arraytype <- paste("package", arraytype, sep = ":") gh <- 
> > > ls(arraytype) gh
> >  [1] "moe430a"              "moe430a_dbconn"       "moe430a_dbfile"
> > "moe430a_dbInfo"       "moe430a_dbschema"     "moe430aACCNUM"
> > "moe430aALIAS2PROBE"   "moe430aCHR"           "moe430aCHRLENGTHS"
> > "moe430aCHRLOC"       
> > [11] "moe430aCHRLOCEND"     "moe430aENSEMBL"
> > "moe430aENSEMBL2PROBE" "moe430aENTREZID"      "moe430aENZYME"
> > "moe430aENZYME2PROBE"  "moe430aGENENAME"      "moe430aGO"
> > "moe430aGO2ALLPROBES"  "moe430aGO2PROBE"     
> > [21] "moe430aMAP"           "moe430aMAPCOUNTS"     "moe430aMGI"
> > "moe430aMGI2PROBE"     "moe430aORGANISM"      "moe430aPATH"
> > "moe430aPATH2PROBE"    "moe430aPFAM"          "moe430aPMID"
> > "moe430aPMID2PROBE"   
> > [31] "moe430aPROSITE"       "moe430aREFSEQ"        "moe430aSYMBOL"
> > "moe430aUNIGENE"       "moe430aUNIPROT"
> >  
> > > gh[33]
> > [1] "moe430aSYMBOL"
> > > 
> > > symbols <- mget(probeids, gh[33])
> > Error in mget(probeids, gh[33]) : second argument must be an 
> > environment
> >  
> > This also doesn't work:
> > > symbols <- mget(probeids, envir=gh[33])
> > Error in mget(probeids, envir = gh[33]) : 
> >   second argument must be an environment
> >  
> > My approach thus is the wrong approach to automatically extract 
> > mappings from a annotation.db.
> > Since i don't know about any other possibility, i would 
> appreciate if 
> > someone could point me to a working solution.
> >  
> > Thanks,
> > Guido
> >  
> > 
> > ------------------------------------------------
> > Guido Hooiveld, PhD
> > Nutrition, Metabolism & Genomics Group Division of Human Nutrition 
> > Wageningen University Biotechnion, Bomenweg 2
> > NL-6703 HD Wageningen
> > the Netherlands
> > tel: (+)31 317 485788
> > fax: (+)31 317 483342 
> > internet:     
> > email:      guido.hooiveld at wur.nl 
> > 
> > 
> > 
> > 	[[alternative HTML version deleted]]
> > 
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