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

[P.D. Moerland]

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 
> 
> 
> 
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