[BioC] question on hgu95 metadata and ontoTools

Elisabetta Manduchi manduchi at pcbi.upenn.edu
Wed Dec 17 22:25:24 MET 2003

thank you very much for such a prompt reply.
A question, with your notation below, shouldn't I do my gets on E5 rather 
than on E1, if E1 is the ancestor? Was that a just typo or am I 
In other words to deal with my case, I guess I could do the following 
(calling hgu95GO my new combined environment):


and then do my gets on hgu95GO, right?

On Wed, 17 Dec 2003, Robert Gentleman wrote:

> On Wed, Dec 17, 2003 at 03:47:54PM -0500, Elisabetta Manduchi wrote:
> > 
> > Hi,
> > I would like to create an environment that combines the hgu95av2GO, 
> > hgu95bGO, ...hgu95eGO into just one environment, that I can subsequently 
> > use as the otkvEnv argument in the ontoTools function otkvEnv2namedSparse.
> > Is there a quick and simple way to do this in R, without having to define 
> > a new hash and the key-value mapping block by block (according to which 
> > environment the key belongs to)? In other words, I'm asking if there is a 
> > one-stop way in R to "union" the above 5 environments.
>  Sort of, in R there are no hash tables but environments are close so
>  we used them. They have a rather unique aspect which is the parent
>  environment. So that if a value is not found in the first environment
>  the parent is searched. So to solve your problem you could do some
>  thing like
>    parent.env(E2) <- E1
>    parent.env(E3) <- E2
>  ...
>   then do your get's on E1 (with inherits=TRUE, which is the default
>   in get) and you should be almost set. The one issue that is not
>   easily solved is the if inherits is TRUE then you search up beyond
>   the last of your environments (your work space and then the search
>   list). But that should not be a problem in your case....
>    Robert
> > Thanks,
> > Elisabetta
> > 
> > _______________________________________________
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> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Elisabetta Manduchi

Computational Biology and Informatics Laboratory
Center for Bioinformatics
University of Pennsylvania
1428 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104-6021

phone: 215-573-4408
fax: 215 573-3111
email: manduchi at pcbi.upenn.edu
web: http://www.cbil.upenn.edu/~manduchi


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