It also seems worth mentioning that the graph package ( http://bioconductor.org/packages/release/bioc/html/graph.html) has reasonable numbers of dependers and importers and could undoubtedly play a role in feature-feature management.
On Sun, Nov 8, 2015 at 8:49 AM, Vincent Carey <st...@channing.harvard.edu> wrote: > In our discussions of the multiassay object/analysis problem, > > https://github.com/vjcitn/biocMultiAssay > > Kasper Hansen has suggested elaborations of the Hits API (see for example > sec. 4 of > > > http://bioconductor.org/packages/release/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf > > , > > more fully described in man pages in S4Vectors > > > http://bioconductor.org/packages/release/bioc/manuals/S4Vectors/man/S4Vectors.pdf > ) > > to manage work on general feature-feature relationships. At present, the > Hits structures/methods > use a pair of integer vectors to collate elements of two objects. Two > general problems that probably need more work are a) classes for feature > annotation elements and b) extensions to Hits that support R idioms for > subsetting collated objects at various points on an analysis path. > > On Sun, Nov 8, 2015 at 8:05 AM, Laurent Gatto <lg...@cam.ac.uk> wrote: > >> >> On 7 November 2015 19:58, Ludwig Geistlinger wrote: >> >> > 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). >> >> I would be delighted to help out in PPI (or Protein-anything >> interactions) infrastructure development, if this is in scope. >> >> Best wishes, >> >> Laurent >> >> > 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 >> >> -- >> Laurent Gatto | @lgatt0 >> http://cpu.sysbiol.cam.ac.uk/ >> http://lgatto.github.io/ >> >> _______________________________________________ >> 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
