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
lklei...@ucr.edu <mailto:lklei...@ucr.edu>
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