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

Aaron Lun alun at wehi.edu.au
Sun Nov 8 20:31:41 CET 2015

Okay, some meat and bones are on GitHub now:


The idea is to represent genomic interactions as pairs of genomic 
regions, using indices to point to a common GRanges object (a la Hits, 
though I haven't used that explicitly due to the presence of additional 
constraints on the indices). Data for each interaction is stored using a 
SummarizedExperiment framework (one row per interaction).

With regards to the methods, most of the low-hanging fruit has been 
implemented, courtesy of inheriting from SummarizedExperiment0. I'll add 
proper unit tests over the coming week. It currently passes through R 
CMD check okay, except for a warning about ":::" in the cbind/rbind 
definitions (callNextMethod() didn't seem to work inside those methods, 
and I didn't want to rewrite the SE0 'binding methods).

Any thoughts appreciated.

- 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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