[Bioc-devel] IGV - a new package in preparation

[Paul Shannon]

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.gabe at 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 <pshannon at 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
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> 
> -- 
> Gabriel Becker, Ph.D
> Scientist
> Bioinformatics and Computational Biology
> Genentech Research