[BioC] Rkeys function from AnnotationDbi returns all Rkeys for a subset

[Hervé Pagès]

The first motivation for keeping keys that are not mapped to
anything was to be backward compatible with the old
environment-based annotations. For example the hgu95av2PMID
map in the hgu95av2 package is a "real" environment containing one
symbol per probeset id. And the value of those symbols that are not
mapped to a PubMed id is set to NA.

This allow all *direct* maps (i.e. maps that go from probeset ids
to some other ids) to have the same set of keys (which is the set
of all probeset ids defined for the chip). I personally find this
to be a nice property because it makes the set of maps defined in
a given package more coherent.

Cheers,
H.


Marc Carlson wrote:
> Laurent Gautier wrote:
>> Inversion of "edge" and "vertex" in parts of my previous email.
>>
>> Some people will have unconsciously corrected it. The others will be
>> very confused.
>>
>> Here is what it should read:
>>
>> Here the subset operation takes a subset of the "mapping", that is of
>> the edges in the bipartite graph, without eliminating the unconnected
>> vertices. I suppose that this choice can be defended by the fact that
>> vertices
>> in an AnnDbBimap object can be without any associated edge, which is
>> making sense. For example, in the context of microarray some probes can
>> be on the array, no given association be associated with it, but yet it
>> is practical to have such probes ID defined in a part (left or right) of
>> the BiMap.
>>
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>>
> 
> I believe that Laurent has the correct interpretation of our motives. 
> These mappings are all based on database joins behind the scenes, so
> frequently it will be the case that things will not be connected, and
> often these unconnected things are of interest (and sometimes they are
> not).  The Lkeys() and Rkeys() functions just give all the left or all
> of the right keys, whether or not they are mapped to anything on the
> other side.  mappedRkeys() and mappedLkeys() are what you want if you
> only want keys that actually "connect" to something. 
> 
> 
>   Marc
> 
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-- 
Hervé Pagès

Program in Computational Biology
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