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

Ludwig Geistlinger Ludwig.Geistlinger at bio.ifi.lmu.de
Sat Nov 7 20:58:41 CET 2015

I agree with Martin, I would love to see something like that.
Especially if this would not be restricted to chromatin interactions, but
also allows to represent protein-protein, transcriptionFactor-targetGene,
miRNA-mRNA etc (e.g. via suitably tailored subclasses).

This might nicely work together with bringing in existing regulatory
networks via AnnotationHub ...

If help is needed, I'm happy to contribute ...


> 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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