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

[Chanchal Kumar]

Dear Dr. Huber,

  Thank you very much for your suggestion. It really helped.

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/
===============================

-----Original Message-----
From: Wolfgang Huber [mailto:huber at ebi.ac.uk] 
Sent: Sunday, December 09, 2007 6:04 PM
To: Chanchal Kumar
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] How to retrieve environment variables from custom
build annotation packages

Dear Chanchal,

try

env = get(paste("ipihs324","ENTREZID",sep=""))
l = mget("IPI00000948",env,ifnotfound=list("FALSE"))
? get

  Best wishes
  Wolfgang


------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

> 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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