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

[Michael Lawrence]

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 <stvjc at channing.harvard.edu>
wrote:

>
>
> 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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>
>

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