[Bioc-devel] deprecating GenomeData and GenomeDataList

[Hervé Pagès]

Hi Michael,

On 05/08/2014 04:35 PM, Michael Lawrence wrote:
> 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, Hervé Pagès <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.
>
>     --
>     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 at fhcrc.org <mailto:hpages at fhcrc.org>
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>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
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>

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