Support for TreeSummarizedExperiment container?

[antagomir]

TreeSummarizedExperiment has emerged as an alternative to phyloseq in R/Bioconductor, using the new SummarizedExperiment container family. There are now couple packages supporting this, e.g. such as curatedMetagenomicData, EBI/MGnify, ANCOMBC etc.

If the qiime2R package is in active stage, we could open a PR adding support to TreeSummarizedExperiment. This could be similar to the current function qiime2R::qza_to_phyloseq i.e. we could contribute qiime2R::qza_to_treese or qiime2R::qza_to_treesummarizedexperiment. This would support linking with an alternative R/Bioc microbiome ecosystem.

[jbisanz]

That sounds like a great idea! Let me know if you want any assistance.

[antagomir]

In practice, this could mean two things to add:

1. qza_to_tse() (similar to the already available qza_to_phyloseq())
2. Adding an example to README (in addition to the already available phyloseq example).
3. Cross-linking to external documentation resources that utilize TreeSE (e.g. OMA gitbook)

We are suggesting a PR soon.

[Insaynoah]

Hi guys, I'm currently working on this function and you can see my progress so far here: added qza_to_tse function.

I tested this on the moving-pictures dataset but I was wondering whether you had some more datasets so I can test and optimise the function even more.

[antagomir]

Thanks @Insaynoah - I suggest that you fork this repo (e.g. your own account or microbiome account), then add a solution there, I can review it and once we are ready you can open the PR here?

[antagomir]

Or perhaps not necessary as the PR is already open. I can comment here directly. Just a need a bit time.

[Insaynoah]

I did indeed fork it. Here you can see the function I added https://github.com/Insaynoah/qiime2R/blob/master/R/qza_to_tse.R

and here's the updated readme file with an example and a link to the oma book : https://github.com/Insaynoah/qiime2R/blob/master/README.md

Thanks in advance for checking.

[antagomir]

Solved in #64 - thanks for all!