[Bioc-devel] BigWigViews

[Valerie Obenchain]

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" <
> kasperdanielhansen at 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.triche at 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 <
>>> kasperdanielhansen at 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.michael at 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
>>>>> <michaelisaiahlove at 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]]
>>>>>>
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>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
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-- 
Valerie Obenchain

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: vobencha at fhcrc.org
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