[Bioc-devel] Call for collaborators/advice

[Tim Triche, Jr.]

Maybe the question arises whether to store a reduced representation like, say, singleCellExperiment does?

In any event, I agree that endomorphism will be expected by users and, like tximport collapsing many transcripts into each gene, the sensible thing to do is just to return a binned (less rows, same columns) version of the input GenomicInteractions object. 

(Also, if this were posted on support.bioconductor.org, Aaron Lun could answer, which is good because he probably already wrote functions to do this at some point.)

--t

> On Mar 22, 2019, at 2:44 PM, Kasper Daniel Hansen <kasperdanielhansen using gmail.com> wrote:
> 
> 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 using 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 using ucr.edu
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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