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

[Leon Yee]

Hi James and Laurent,


James W. MacDonald wrote:
> Hi Leon,
> 
> Leon Yee wrote:
>> Dear all,
>>
>>      I encountered a problem when I using Rkeys from AnnotationDbi
>> package. Using [] I get a subset of a AnnDbBimap object, but when I
>> using Rkeys for this subset, it returns all of the Rkeys from the
>> original set.
> 
> I don't believe Rkeys() is intended to return a subset - it is intended 
> to give you all the right keys of the object. But I am not sure why you 
> want to use Rkeys() to do what you have already done using 
> as.list(hgu95av2PATH[ids]). Perhaps I misunderstand?
> 

   Yes, as Laurent pointed out, mappedRkeys() is what I'm looking for. I 
just feel that Rkeys() is semantically somewhat misleading according to 
its name , you know, Lkeys() just returns the Lkeys of the subset 
(including NAs), while Rkeys() returns all of the Rkeys of the whole 
set.  Or maybe "[]" is not a real subsetting operation?


   Thank you very much.

Best regards,
Leon