I'm happy to contribute as well. We will send something along.
Best, Mike On Nov 18, 2013 8:09 PM, "Kasper Daniel Hansen" < kasperdanielhan...@gmail.com> wrote: > tileGenome? > > Michael, making us do a prototype in R is a very reasonable request. We > should do that. > > Best, > Kasper > > > On Mon, Nov 18, 2013 at 7:45 PM, Tim Triche, Jr. <tim.tri...@gmail.com > >wrote: > > > Doesn't tileGenome or whatever it's called help with the binning? It's > > not too hard to bolt multiple tracks into a SummarizedExperiment at that > > point. > > > > --t > > > > > On Nov 18, 2013, at 4:33 PM, Kasper Daniel Hansen < > > kasperdanielhan...@gmail.com> wrote: > > > > > > (Michael Love and I had some discussion on this Friday) > > > > > > I also think it would be a very convenient class/method. A lot of data > > > these days are naturally represented (and are available from say GEO) > as > > > bigWig files (essentially coverage tracks), for example ChIP-seq. This > > > would be much more efficient than converting BAM to coverage on the > fly. > > > > > > It seems to me that bigWig ought to be efficient for this, but I am not > > > very familiar with its performance. What we want is really to be able > to > > > chunk multiple coverage profiles over the genome, and do computations > on > > > each of the chunks. Any idea on efficiency? I am happy to contribute > a > > > bit, at least with design. > > > > > > Best, > > > Kasper > > > > > > > > > On Mon, Nov 18, 2013 at 6:11 PM, Michael Lawrence < > > lawrence.mich...@gene.com > > >> wrote: > > > > > >> Aggregating coverage over multiple samples is a popular request > > recently. > > >> I'm happy to support this effort, but I thinks someone in Seattle is > > going > > >> to have to take the lead on it. > > >> > > >> > > >> On Mon, Nov 18, 2013 at 2:36 PM, Michael Love > > >> <michaelisaiahl...@gmail.com>wrote: > > >> > > >>> a discussion came up on devel last year about looking at a genomic > > range > > >>> over multiple samples and multiple experiments ( > > >> > > > https://stat.ethz.ch/pipermail/bioc-devel/attachments/20120920/93a4fb61/attachment.pl > > >>> ) > > >>> > > >>> stepping aside the multiple experiment part, I'm interested in > > >>> BigWigViews() with fixed ranges across samples. Has there been any > more > > >>> thoughts in this direction? > > >>> > > >>> BigWigViews would be incredibly useful for genomics applications > where > > we > > >>> want to scan along the genome looking at lots of samples. BigWig > > offers a > > >>> concise representation of the information compared to BAM files. > > >>> > > >>> What I am trying now is using import(BigWigFile, which=gr) on files > one > > >> by > > >>> one, and then binding the coverage together. > > >>> > > >>> best, > > >>> > > >>> Mike > > >>> > > >>> [[alternative HTML version deleted]] > > >>> > > >>> _______________________________________________ > > >>> 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 > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
