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
appreciated.
Cheers,
Aaron
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-boun...@r-project.org] on behalf of Aaron
Lun [a...@wehi.edu.au]
Sent: Thursday, November 05, 2015 12:27 PM
To: bioc-devel@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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