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 
... ???)

  thanks a lot for your help,

  Arne




	[[alternative HTML version deleted]]