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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