[Bioc-devel] deprecating GenomeData and GenomeDataList

Hi Michael,
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.
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.

On Thu, May 8, 2014 at 3:32 PM, Herv? Pag?s <hpages at fhcrc.org
<mailto:hpages at 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.

    --
    Herv? Pag?s

    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 at fhcrc.org <mailto:hpages at fhcrc.org>
    Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
    Fax: (206) 667-1319 <tel:%28206%29%20667-1319>

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Herv? Pag?s

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 at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

[Bioc-devel] deprecating GenomeData and GenomeDataList

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