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

Aaron Lun alun at wehi.edu.au
Thu Nov 5 18:27:04 CET 2015

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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