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 > On Mar 7, 2018, at 2:40 PM, Gabe Becker <becker.g...@gene.com> wrote: > > Paul, > > Sounds cool! My one note after a quick first pass is that here: > > On Wed, Mar 7, 2018 at 2:15 PM, Paul Shannon <pshan...@systemsbiology.org> > wrote: > Note that though igv.js typically gets its track data from CORS/indexed > webservers, the IGV package will also support locally created R data.frames > describing either bed or wig tracks - annotation and quantitative, > respectively - without any need to host those tracks on a pre-existing > webserver. httpuv includes a minimal webserver which can adequately serve > the temporary files IGV creates from your data.frames. > > It seems to me that those data.frames should be replaced with the core > Bioconductor object classes which represent the types of information being > displayed. You might look to epivizr for inspiration here, which (IIRC) > allows "tracks" within epiviz to be backed by bioconductor objects. > > Best, > ~G > > > - Paul > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > -- > Gabriel Becker, Ph.D > Scientist > Bioinformatics and Computational Biology > Genentech Research _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
