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 <[email protected]> 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 [[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 > >> > > > > _______________________________________________ > > [email protected] mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > -- > Laurent Gatto | @lgatt0 > http://cpu.sysbiol.cam.ac.uk/ > http://lgatto.github.io/ > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
