The chipseq package still uses them. There is a method on
estimate.mean.fraglen, and both subsetSummary() and laneSubsample() expect
one. We can remove the estimate.mean.fraglen and subsetSummary functions,
as they have been deprecated for years. laneSubsample() might be useful? I
don't think it's worth my time porting...

I fixed the documentation of data(cstest): it is indeed a GRangesList now.




On Thu, May 8, 2014 at 4:58 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> 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@fhcrc.org
>> <mailto: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 <mailto:hpages@fhcrc.org>
>>     Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>>     _________________________________________________
>>     Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing
>> list
>>     https://stat.ethz.ch/mailman/__listinfo/bioc-devel
>>     <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>
>>
>>
> --
> 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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