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 <a...@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-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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
