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

[Malcolm Perry]

Our package, GenomicInteractions, was designed partly with this goal in
mind. The latest version is in Bioc release and on github (
https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions).

We've represented interactions using two different sets of anchors, with an
additional 'counts' label, and the class is based around Vector since it
was intended as a rough equivalent to GRanges. All of the usual methods
(subsetting, sorting, mcols, overlaps etc.) are there as well as export and
import for a number of interaction file formats and some functions for
analysis.

Malcolm

On Sun, Nov 8, 2015 at 7:31 PM, Aaron Lun <alun at wehi.edu.au> 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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