There may be a common pattern emerging where derivatives of SummarizedExperiment add support for specific feature types. Currently, we have ranges, and it was suggested in a package submission thread to support gene sets (or pathways, etc). Those could also be represented by a graph, or something more specific.
On Thu, Oct 19, 2017 at 8:06 AM, Vincent Carey <st...@channing.harvard.edu> wrote: > > > On Thu, Oct 19, 2017 at 10:12 AM, Levi Waldron < > lwaldron.resea...@gmail.com> wrote: > >> Thanks for all your thoughts Joey, and I hope I didn't come across as >> ... >> >> On Wed, Oct 18, 2017 at 11:36 PM, Paul Joseph McMurdie <joey...@gmail.com >> > >> wrote: >> >> ... >> >> > - There actually *still isn't core support for evolutionary trees in >> BioC* (as >> > mentioned by Joe Paulson and Ben Callahan in other threads). One of >> > phyloseq's key contributions was to leverage the fantastic >> representation >> > of trees implemented in the CRAN package "ape" in order to support >> analysis >> > techniques popular among microbiome researchers that require a >> phylogenetic >> > tree. The integration in the phyloseq-class and ape is necessarily >> pretty >> > deep, including certain row operations. Users also needed a familiar and >> > simple R interface to manipulate that composite object despite the >> complex >> > hierarchical relationship among rows. Correct me if I'm wrong, but I >> think >> > there is still no core BioC support for representing tree-like or >> > bio-taxonomy-like hierarchy among rows in a SummarizedExperiment, or >> > equivalent; and consequently certain row operations may have to be >> modified >> > more deeply than usual if we were to re-implement phyloseq "the right >> way". >> > I'd love to hear thoughts on this. >> > >> >> AFAIK you're right, and I don't know the solution, although I hope it can >> be built on SummarizedExperiment. Looking forward to talking more about >> this. >> > > Yes. Let's write up the use cases and try to spec something out. Maybe > start a topic on the support site, or a slack channel? rowRanges seems > very useful, perhaps > a rowGraph/colGraph concept would be useful too. Establishing idioms for > using > these in model specification would be nice. > > >> >> >> > Even though phyloseq is at the receiving end, I think the criticism is >> > fair, and I want current and future new BioC contributors to not >> re-make my >> > mistakes circa 2011-12. I'm happy to help if I can. >> > >> > Cheers, and thanks for the interesting, collegial thread. >> > >> > Joey >> > >> >> Thanks Joey, and I do want to say also that I think phyloseq is >> responsible >> for making Bioconductor a viable and already superior choice for >> statistical analysis of microbiome data! >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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
