On 10/19/2017 11:06 AM, Vincent Carey 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.
I started a slack channel for this; all are welcome to participate but I
don't know how to invite people
I believe people can join the Bioconductor community by visiting
https://bioc-community.herokuapp.com/
Martin
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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