[Bioc-devel] deprecating GenomeData and GenomeDataList

Hervé Pagès hpages at fhcrc.org
Fri May 9 00:32:33 CEST 2014


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.


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

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