[Bioc-devel] Why should Bioconductor developers re-use core classes?

[Vincent Carey]

On Thu, Oct 19, 2017 at 10:12 AM, Levi Waldron <lwaldron.research at 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 <joey711 at 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!
>
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>
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