[BioC] How to retrieve environment variables from custom build annotation packages

Chanchal Kumar chanchal at biochem.mpg.de
Sun Dec 9 17:50:49 CET 2007


Dear Bioconductor Developers and Users,

   I have a custom annotation package which I created using "AnnBuilder"
package. The package named "ipihs324" has annotation for IPI identifiers
and contains mappings to Entrez ids in the environment variable
ipihs324ENTREZID.

Now when I provide this environment directly like :
l <- mget("IPI00000948",ipihs324ENTREZID,ifnotfound=list("FALSE"))

then I get result.

> l
$IPI00000948
[1] 26608

But if I try as following:
> env<-paste("ipihs324","ENTREZID",sep="")

> l <- mget("IPI00000948",env,ifnotfound=list("FALSE"))

I get this error:
##########################
Error in mget("IPI00000948", env, ifnotfound = list("FALSE")) : 
  second argument must be an environment
##########################

As I want to write a generic code for loading any data package and then
retrieve its environment for Entrez ids mappings, so I need to do it
this second way. Can anyone suggest how to convert the string type to an
environment type? I have tried as.environment() but that too doesn't
work. Any suggestions and comments will be very helpful. 

Best Regards,
Chanchal 
===============================
Chanchal Kumar, Ph.D. Candidate
Dept. of Proteomics and Signal Transduction
Max Planck Institute of Biochemistry
Am Klopferspitz 18
82152 D-Martinsried (near Munich)
Germany
e-mail: chanchal at biochem.mpg.de
Phone: (Office) +49 (0) 89 8578 2296
Fax:(Office) +49 (0) 89 8578 2219
http://www.biochem.mpg.de/mann/
===============================



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