[Bioc-devel] Call for collaborators/advice
|n||n|te@monkey@@w|th@keybo@rd@ @end|ng |rom gm@||@com
Wed Apr 3 06:54:08 CEST 2019
> 1) A package to define a base (virtual) "Interactions" class. This would
> basically have a constant "Vector" store with a "Hits" object specifying
> the pairwise interactions between elements in the constant store. One
> could also distinguish between "SelfInteractions" (constant store) and
> the more general "Interactions" (two stores, possibly of different
> types, e.g., genomic interval -> protein interactions). A variety of
> methods would be available here to do manipulations and such.
> 2) A package to define an "Interactions" subclass where the store is a
> genomic interval, with basic methods to operate on such classes. Methods
> such as findOverlaps(), linkOverlaps() and boundingBox() would probably
> go here. @Luke, a binning method could also conceivably go here.
> All of this is open for discussion, if people are interested and willing
> to volunteer. These changes will not make the next release anyway.
What he said.
> On 22/03/2019 19:54, Aaron Lun wrote:
>> Hi Luke,
>> Do you mean bins or bin pairs?
>> If you want to just bin the coverage in terms of the linear genome,
>> there should be ways to do that outside of InteractionSet or
>> GenomicInteractions. This is just dealing with standard genomic
>> interval data; extract the anchor coordinates and plug it in elsewhere.
>> If you want to collate region pairs into bin pairs; I don't know of a
>> dedicated function to do this from a GInteractions object (diffHic
>> only does this from raw read data). You'll need to figure out what to
>> do to regions that cross bin boundaries.
>> The simplest way to mimic this behaviour right now is to generate
>> another GInteractions object containing ALL POSSIBLE bin pairs (use
>> combn with a constant set of bin regions) and plug that into
>> countOverlaps. This will generate loads of zeroes, though, so is not
>> the most efficient way to do this. You could get a sparser form with
>> linkOverlaps but this requires more work to get the counts.
>> I have some more thoughts about the Bioconductor Hi-C infrastructure,
>> but my laptop battery's running out and I left my charger in my new
>> apartment. So that'll have to wait until tomorrow.
>> On 22/03/2019 09:31, Luke Klein wrote:
>>> I am writing a package that will extend the GenomicInteractions
>>> class. I am a statistician, so I may not know best practices when
>>> it comes to extending existing classes (eg. should I make a new slot
>>> or simply add a column to the `elementMetadata`? Are there existing
>>> functions that already do what I am attempting?).
>>> I am not familiar with Bioc-Devel decorum, so if asking this here is
>>> inappropriate, kindly let me know.
>>> About my project:
>>> In the first step, I am hoping to implement a HiC binning function on
>>> HiC data contained in a GenomicInteractions set. I aim to:
>>> - Reorder the anchor pairs (I will explain in more detail to anyone
>>> that wants to help)
>>> - Collapse the regions to the desires bin width
>>> - Sum the counts within each bin
>>> - Update the anchors to agree with the new/updated regions
>>> This will set the stage for the new class that I hope to create for
>>> HiC domain calling, but I need to achieve the above tasks first.
>>> All the best to everyone!
>>> —*Luke Klein*
>>> PhD Student
>>> Department of Statistics
>>> University of California, Riverside
>>> lklei001 using ucr.edu <mailto:lklei001 using ucr.edu>
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