[Bioc-devel] Call for collaborators/advice

Aaron Lun |n||n|te@monkey@@w|th@keybo@rd@ @end|ng |rom gm@||@com
Sat Mar 23 03:54:00 CET 2019

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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