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 wrote:
> Hi Mike (and others),
>
> I've started a package called GenomicFileViews on our github site:
>
> https://github.com/Bioconductor/
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 pri
I guess the point is we want to see what kind of analyses can be supported
by streaming along the genome, and avoiding intermediate files for each
sample. But maybe that's not ideal for your case, where you add a single
sample and then have to repeat some summarization task at the level of
individu
Hi,
I just went through this approach in yeast,
regions = gene promoters
assays = H3K3ME1, H3K3ME2, H3K3ME3 ChipSeq
experimental conditions: 7 recombinant knock-outs and knock-ins of
different domains of different genes.
two replicates
So, what I first
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
>
>
>
tileGenome would generate the ranges if you wanted to regular bins over
some part of the genome. Not sure what you use case is. But generating the
ranges is probably the easy part.
On Mon, Nov 18, 2013 at 5:08 PM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:
> tileGenome?
>
> Mich
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. wrote:
> Doesn't tileGenome or whatever it's called help with the binning? It's
> not too hard to bolt multiple tracks into a Summ
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
> wrote:
>
> (Michael Love and I had some discussion on this Friday)
>
> I also thi
Retrieving the data for a genomic range is efficient, doing this for
thousands of samples might get tricky, but could probably be vectorized
through clever use of matrices. But millions of regions by thousands of
samples might need some support in native code, along the lines of
viewSums, etc, but
(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 effici
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
wrote:
> a discussion came up on devel last year about looking at a g
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
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