[BioC] org.*.eg.db problem

[Martin Morgan]

On 12/01/2010 08:48 AM, arne.mueller at novartis.com wrote:
> Hello,
> 
> the org.*.eg.db environments cannot be used in a generic way :-( . Let's 
> say I'm writing a function that needs an entire org.*.eg.db environment as 
> argument, and the function doesn't care whether it's human, mouse rat or 
> jellyfish. Inside my function I'd be required accessing the maps (e.g. for 
> chromosomal location) without knowing the species. The problem is that you 
> do need to know the species because the mapping names use the species 
> abbreviation:
> 
>> org.Mm.egCHRLOC
> CHRLOC map for Mouse (object of class "AnnDbMap")
> 
> Why isn't this more generic so that one could just call egCHRLOC instead 
> of org.Mm.egCHRLOC which makes code that uses this annotation having to 
> know about the organism - why does it have to be be hard coded? Ideally 
> I'd like to be able to do the following:
> 
>> library(org.Mm.eg.db) 
>> myGenomeAnnotationFunction(org.Mm.eg.db)  { # pass in as an environment?
>       # use the annotation environment to extract whatever information ...
> }
> 
> How would you solve this when having to work with several species (if else 
> ... ???)
> 


Hi arne --

For many cases,

library(annotate)
map <- getAnnMap("CHRLOC", "org.Mm.eg.db")

which will take care of loading the org package as well.

Martin


>   thanks a lot for your help,
> 
>   Arne
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793