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
