[Bioc-devel] Base class for interaction data - expressions of interest

Aaron Lun alun at wehi.edu.au
Sun Nov 8 14:40:13 CET 2015

Thanks for the interest, everyone. I'll try to put up what I've 
currently got onto my GitHub page, sometime over the week.

Currently, I'm calling it an "InteractionSet" object; it builds off the 
SummarizedExperiment0 class and adds some stuff to handle pairwise 
genomic interactions.

- Aaron

On 07/11/15 19:33, Morgan, Martin wrote:
> Just to say that this is a great idea. If this starts as a github package (or in svn, we can create a location for you if you'd like) I and others would I am sure be happy to try to provide any guidance / insight. The main design principles are probably to reuse as much as possible from existing classes, especially the S4Vectors / GRanges world, and to integrate metadata as appropriate (like SummarizedExepriment, for instance).
> Martin
> ________________________________________
> From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Aaron Lun [alun at wehi.edu.au]
> Sent: Thursday, November 05, 2015 12:27 PM
> To: bioc-devel at r-project.org
> Subject: Re: [Bioc-devel] Base class for interaction data - expressions of      interest
> There's a growing number of Bioconductor packages dealing with
> interaction data; diffHic, GenomicInteractions, HiTC, to name a few (and
> probably more in the future). Each of these packages defines its own
> class to store interaction data - DIList for diffHic,
> GenomicInteractions for GenomicInteractions, and HTClist for HiTC.
> These classes seem to share a lot of features, which suggests that they
> can be (easily?) replaced with a common class. This would have two
> advantages - one, developers of new and existing packages don't have to
> continually write and maintain new classes; and two, it provides users
> with a consistent user experience across the relevant packages.
> My question is, does anybody have anything in the pipeline with respect
> to a base package for an interaction class? If not, I'm planning to put
> something together for the next BioC release. To this end, I'd welcome
> any ideas/input/code; the aim is to make a drop-in replacement (insofar
> as that's possible) for the existing classes in each package.
> Cheers,
> Aaron
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