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

Aaron Lun alun at wehi.edu.au
Mon Nov 16 10:33:19 CET 2015

Hello all,

I thought I might give an update on the state of affairs for the 
InteractionSet package. Currently, there's three classes:

- the GInteractions class, inheriting from Vector and intended to 
represent pairwise interactions between genomic regions (based on 
suggestions from Malcolm Perry and Liz Ing-Simmons).

- the InteractionSet class, inheriting from SummarizedExperiment0 and 
containing a GInteractions object; intended to store experimental data 
about pairwise interactions (one interaction per row).

- the ContactMatrix class, inheriting from Annotated and storing data in 
matrix form (where rows/columns represent genomic regions).

Getters, setters, conversion methods between classes, distance 
calculation methods and overlap methods have been implemented. Man pages 
and "testthat" scripts have also been written. Still missing a vignette, 
though it should be easy enough to write one.

All in all, I think it's a solid first draft. Any comments would be 



On 08/11/15 19:31, Aaron Lun wrote:
> Okay, some meat and bones are on GitHub now:
> https://github.com/LTLA/InteractionSet
> 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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