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

Morgan, Martin Martin.Morgan at roswellpark.org
Sat Nov 7 20:33:18 CET 2015

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).

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.



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