[BioC] Bioconductor Digest, Vol 104, Issue 7

[Stefan McKinnon Høj-Edwards]

Hi Iain,

I also had problems with the org.Xx.eg.db packages and ended up making a package, AnnotationFuncs, for it. It handles mapping from one identifier to another (via the central identifier), using the data packages. I have included an example below.

> library(AnnotationFuncs)
> library(org.Hs.eg.db)
> syms <- c('ACTB', 'TNF', 'TGFB1')
> translate(syms, from=org.Hs.egSYMBOL2EG, to=org.Hs.egENSEMBL)
$ACTB
[1] "ENSG00000075624"

$TNF
[1] "ENSG00000204490" "ENSG00000206439" "ENSG00000223952" "ENSG00000228321"
[5] "ENSG00000228849" "ENSG00000230108" "ENSG00000232810"

$TGFB1
[1] "ENSG00000105329"


Kind regards

Stefan McKinnon Høj-Edwards              Dept. of Molecular Biology and Genetics
Ph.D. Fellow                             Aarhus University
                                         Blichers Allé 20, Postboks 50
                                         DK-8830 Tjele
Tel.: +45 8715 7969                      Tel.: +45 8715 6000
Email: Stefan.Hoj-Edwards at agrsci.dk      Web: www.agrsci.dk



-----Oprindelig meddelelse-----
Message: 4
Date: Thu, 6 Oct 2011 12:50:41 +0100
From: Iain Gallagher <iaingallagher at btopenworld.com>
To: bioconductor <bioconductor at stat.math.ethz.ch>
Subject: [BioC] mapping through org.Xx.eg.db packages
Message-ID:
	<1317901841.98063.YahooMailClassic at web86708.mail.ird.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Dear List

I wonder is someone could shed some light on the following.

Given a set of gene symbols I would like to retrieve different identifiers. 

Using the org.Xx.eg.db packages I can go about this by mapping through the EntrezIDs:

# mapping through eg ids as package is eg id centric
library(org.Hs.eg.db)
syms <- c('ACTB', 'TNF', 'TGFB1')
egID <- unlist(mget(syms, org.Hs.egSYMBOL2EG, ifnotfound=NA))
ensID <- unlist(mget(egID, org.Hs.egENSEMBL, ifnotfound=NA))

> ensID
               60             71241             71242             71243 
"ENSG00000075624" "ENSG00000204490" "ENSG00000206439" "ENSG00000223952" 
            71244             71245             71246             71247 
"ENSG00000228321" "ENSG00000228849" "ENSG00000230108" "ENSG00000232810" 
             7040 
"ENSG00000105329" 

> egID
  ACTB    TNF  TGFB1 
  "60" "7124" "7040" 

Now here I assumed that the names of the ensID object were the original EntrezIDs mapped from the symbols but because R does not handle duplicate names they are not - with renumbering for those EntrezIDs that have a plurality of matches (here 7124 becomes 71241, 71242 etc etc)

This has caused me some confusion since each of these names is an actual Entrez ID - just not one I'm interested in.

The same can happen when mapping from any ID that ends in a numeric part (eg Ensembl ids). 

It is useful to return a mapping showing the original identifier, the EntrezID mapped through and the required identifier so how could one reliably do this when mapping through e.g. Entrez IDs as in the method above (i.e. return the Entrez ID and Ensembl ID in one sweep)?

I have tried using the SQL approach:

dbCon <- org.Hs.eg_dbconn()
sqlQuery <- 'SELECT * FROM genes, gene_info, ensembl WHERE genes._id = gene_info._id = ensembl._id;'
result <- dbGetQuery(dbCon, sqlQuery)

where one could filter the 'result' object with the symbols of interest but this query takes a long time to run. I know little SQL so that might be an issue!

Best

iain