[BioC] org.*.eg.db problem

[Iain Gallagher]

You could write in a check and use 'with'.

if 'mouse' 

yourFunction (with (org.Mm.eg.db... etc etc))

if 'human'

yourFunction (with (org.Hs.eg.db... etc etc))

This might not be optimal as I'm not a programmer by any measure (!) but it's one way to get what I think you want.

cheers

iain

--- On Wed, 1/12/10, Laurent Gautier <laurent at cbs.dtu.dk> wrote:

> From: Laurent Gautier <laurent at cbs.dtu.dk>
> Subject: Re: [BioC] org.*.eg.db problem
> To: arne.mueller at novartis.com
> Cc: bioconductor at stat.math.ethz.ch
> Date: Wednesday, 1 December, 2010, 17:28
> On 01/12/10 17:50, Martin Morgan
> wrote:
> > 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:
> >>
> 
> This is likely a design decision forced by R's scoping rule
> for attached 
> packages: attaching a package will bring its (exported)
> content into the 
> search path.
> In other words, if you would have a package org.Mm.eg.db
> and a package 
> org.Hs.eg.db, both containing an object egCHRLOC, the
> symbol egCHRLOC 
> would be resolved to two different things depending on
> which one of the 
> two packages was attached last.
> 
> This does prevent some of the patterns frequently found in
> other 
> language from being (safely) implemented
> (and is unfortunate).
> 
> 
> >>> 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]]
> >>
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> >
> 
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