Sounds good. Somewhat related: it would be nice to have an lapply method
for BSgenome that iterates over the chromosomes, but bsapply would work
just fine returning a list.


On Thu, May 8, 2014 at 3:32 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> 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
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
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