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[Bioc-devel] deprecating GenomeData and GenomeDataList

6 messages · Dario Strbenac, Hervé Pagès, Michael Lawrence

Original
Hervé Pagès
# 
Hi,

I'd like to deprecate the GenomeData and GenomeDataList classes defined
in the BSgenome package. If you've never heard about these containers,
you can stop reading here.

I was able to find only 2 BioC packages that "use" these classes:
oneChannelGUI and Repitools. It doesn't seem to me that these
packages are actually creating/using GenomeData or GenomeDataList
objects in their examples or vignettes. All they do is implement
some low-level utilities (reformatGdl in oneChannelGUI, GDL2GRL in
Repitools) to convert a GenomeDataList into something else. Also I
couldn't find any place where these utilities are actually used.

Note that GenomeData/GenomeDataList predate GRanges/GRangesList
and it seems that most of the times (if not every time) the latters
can be used instead of the formers. Please let me know if you have
a use case where you think there are significant benefits in using
GenomeData/GenomeDataList over GRanges/GRangesList.

Thanks,
H.
Hervé Pagès
# 
Hi Michael,
On 05/08/2014 04:35 PM, Michael Lawrence wrote:
Yes, that's the plan. In the immediate future modify bsapply() to return
an ordinary list. Then later add an "lapply" method for BSgenome and
maybe get rid of bsapply() at some point.

BTW, in my quest for packages that use the GenomeData/GenomeDataList
objects, I ran into the chipseq package, which, IIRC, used to be the
first consumer of these objects and was the original motivation for
introducing them. However it seems that theses days the package doesn't
use them anymore (looks like it uses GRanges/GRangesList instead) even
though the documentation still mentions them everywhere. Any chance the
doc could be updated?

Thanks,
H.

  
    

      
      
    

  


  


      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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On 05/08/2014 05:00 PM, Dario Strbenac wrote:

            

      
      
      
    

        
Sounds good.

H.