Message-ID: <CAC2h7utVvHXR0+GHx37QBNx4=aq5pSdvNZpQjkDhNA2F9HP3gQ@mail.gmail.com>
Date: 2019-03-22T18:44:43Z
From: Kasper Daniel Hansen
Subject: [Bioc-devel] Call for collaborators/advice
In-Reply-To: <0B858112-7EB6-4A52-8A92-1C776FD65B43@ucr.edu>
Why is this not "just" a function which transforms one GI into another GI?
Thats what it seems to me.
On Fri, Mar 22, 2019 at 12:31 PM Luke Klein <lklei001 at ucr.edu> 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 at ucr.edu
>
>
>
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