Metoo. This is becoming an item of major interest for some treatment biomarkers we are studying.
--t > On Nov 7, 2015, at 11:33 AM, Morgan, Martin <martin.mor...@roswellpark.org> > 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
