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 <hpa...@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 <hpa...@fhcrc.org >> <mailto: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 <mailto:hpa...@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: hpa...@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]
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