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

Marc Carlson mcarlson at fhcrc.org
Wed Dec 10 18:05:48 CET 2008

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. 


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