I agree with Martin, I would love to see something like that. Especially if this would not be restricted to chromatin interactions, but also allows to represent protein-protein, transcriptionFactor-targetGene, miRNA-mRNA etc (e.g. via suitably tailored subclasses).
This might nicely work together with bringing in existing regulatory networks via AnnotationHub ... If help is needed, I'm happy to contribute ... Best, Ludwig > 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 > > _______________________________________________ > Bioc-devel@r-project.org 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. > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
