On Thu, Mar 8, 2018 at 12:29 AM, Paul Shannon <pshan...@systemsbiology.org> wrote:
> Thanks, Gabe. > > You make an excellent point: bioc objects get first class support. In > some instance, base R data types deserve that also, and data.frames lead > the list for me, being useful, concise, universally available, expressive. > > So perhaps not “data.frames replaced by” but “accompanied by” appropriate > bioc data types? > > - Paul > Definitely +1 for supporting GenomicRanges, including what's in genome() and mcols(). There's a demo of an rtracklayer -> GRanges -> UCSC genome browser workflow in the rtracklayer vignette <http://bioconductor.org/packages/release/bioc/vignettes/rtracklayer/inst/doc/rtracklayer.pdf> that I've made use of. I wouldn't necessarily say *don't* support data.frame, but I would certainly encourage Bioc users to import data with rtracklayer instead of generic read* functions, and to take advantage of the vast AnnotationHub and OrganismDbi-based annotations which provide GenomicRanges objects. Thanks and looking forward to it! [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
