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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
