Hi,
> -----Original Message----- > From: Bioc-devel <bioc-devel-boun...@r-project.org> On Behalf Of > Michael Lawrence > Sent: Friday, March 09, 2018 1:49 PM > To: Paul Shannon <pshan...@systemsbiology.org> > Cc: Gabe Becker <becker.g...@gene.com>; bioc-devel@r-project.org > Subject: Re: [Bioc-devel] IGV - a new package in preparation > > Couple of things: > > 1) Check out epivizr and the surrounding infrastructure (maybe Hector can > chime in). It's able to serve up data directly from R; would be nice if we > could do that with IGV, instead of writing out to files. That would require > it to talk to some standard API, like the old DAS. One value of writing to files is that if IGV is running on remote host then retrieval via byte-range encoding continues to just work. Of course this is dependent upon what you are trying to do. ~malcolm_c...@stowers.org > > 2) The rtracklayer API is in rtracklayer/R/browser.R. See ucsc.R for how > that is implemented for UCSC. > > On Fri, Mar 9, 2018 at 9:59 AM, Paul Shannon > <pshan...@systemsbiology.org> > wrote: > > > Thanks, Levi. Your comments, and Gabe’s are very helpful, getting me to > > consider things I have overlooked. > > > > Support for GenomicRanges is essential, as you and Gabe point out. > > > > In all cases IGV will convert a GRanges object to an appropriate track, > > then write it out as a temporary file. igv supports bed, gff, gff3, gtf, > > wig, bigWig, bedGraph, bam, vcf, and seg formats, and a variety of > > sources: files via http, google cloud storage, GA4GH; recent limited > > support has been provided for direct javascript data. Maybe someday > > AnnotationHub? > > > > GenomicRanges as I understand them are very flexible, not subclassed > into > > types as are track formats. So I propose that in many cases it will be he > > user’s responsibility to specify track type, call the appropriate > > constructor, maybe specify column names so that the right scores can be > > extracted from the mcols - whose names are, so far as I know, are not > > standardized. > > > > If the GRanges object is too big - greater than a densely packed > megabase, > > for instance, igv works best if the track file is indexed and served up by > > an index- and CORS-savvy webserver. Thus the IGV should politely fail - > > or at least issue a warning - when encounters big tracks. This “too big” > > threshold may change over time. > > > > Reading through Michael’s rtracklayer vignette I came across this: > > > > The rtracklayer package currently interfaces with the UCSC web-based > > genome browser. > > Other packages may provide drivers for other genome browsers through > a > > plugin system. > > > > Can anyone (maybe Michael himself?) comment on how I can evaluate an > > rtracklayer plugin strategy for igv? > > > > - Paul > > > > > > > On Mar 9, 2018, at 4:15 AM, Levi Waldron > <lwaldron.resea...@gmail.com> > > wrote: > > > > > > 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 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! > > > > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
