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
