[Bioc-devel] Call for collaborators/advice

Aaron Lun |n||n|te@monkey@@w|th@keybo@rd@ @end|ng |rom gm@||@com
Wed Apr 3 06:54:08 CEST 2019

Breaker breaker.

> 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.

https://github.com/LTLA/IndexedRelations (WIP)

> 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.
>> -A
>> 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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