hi Valerie, That's great. Yes I will add it in as BigWigFileViews. I am mikelove on github.
best, Mike On Tue, Dec 24, 2013 at 11:44 AM, Valerie Obenchain <voben...@fhcrc.org>wrote: > Hi Mike (and others), > > I've started a package called GenomicFileViews on our github site: > > https://github.com/Bioconductor/GenomicFileViews > > The idea is to provide infrastructure for parallel execution over a group > of common file types either 'by file' or 'by range'. I realize this thread > is primarily concerned with 'by range' over BigWig but we'd like to support > Bam, Fasta, VCF and maybe others? > > I've started development on BamFileViews and FaFileViews classes. It would > be great if you could add your work on BigWig to this package - maybe as > BigWigFileViews. Please send me your git username I'll give you permissions. > > This is in the early stages but you can get an idea of where we're going. > Feedback welcome. > > Thanks. > Valerie > > > > On 11/18/2013 05:12 PM, Michael Love wrote: > >> 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 >> >> > > -- > Valerie Obenchain > > Program in Computational Biology > Division of Public Health Sciences > > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B155 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: voben...@fhcrc.org > Phone: (206) 667-3158 > Fax: (206) 667-1319 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
