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 <hpa...@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: hpa...@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]]
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