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
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--
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
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