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

[Martin Morgan]

Hooiveld, Guido wrote:
> 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?

Hi Guido --

to get the appropriate map

  library(annotate)
  map = getAnnMap("SYMBOL", annotation(eset))

to select just the relevant probes

  map[probeids]

toTable(map[probeids]) or as.list(map[probeids]) might be the next step
in the work flow.

Martin

>  
> 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:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
> email:      guido.hooiveld at wur.nl 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor