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