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
> On Mar 7, 2018, at 2:40 PM, Gabe Becker <becker.g...@gene.com> wrote:
> 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>
> 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.
> - Paul
> Biocfirstname.lastname@example.org mailing list
> Gabriel Becker, Ph.D
> Bioinformatics and Computational Biology
> Genentech Research
Biocemail@example.com mailing list