Thanks for the interest, everyone. I'll try to put up what I've
currently got onto my GitHub page, sometime over the week.
Currently, I'm calling it an "InteractionSet" object; it builds off the
SummarizedExperiment0 class and adds some stuff to handle pairwise
genomic interactions.
- 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 [[email protected]] on behalf of Aaron Lun
[[email protected]]
Sent: Thursday, November 05, 2015 12:27 PM
To: [email protected]
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
_______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited. If you have received
this message in error, please notify the sender immediately by e-mail and
delete this email message from your computer. Thank you.
_______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
