FEAT: ANCOM-BC R wrapper

qiime2 / q2-composition

BSD 3-Clause "New" or "Revised" License

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FEAT: ANCOM-BC R wrapper #88

Closed lizgehret closed 1 year ago

lizgehret commented 2 years ago

New method in q2-composition that wraps the ANCOM-BC functionality from this R package. I used some of @mortonjt's ideas from his q2-ancombc plugin, but added some additional guards, and have wrapped up the outputs differently.

The contents of this PR include:

New method ancombc that produces an artifact containing the following:
- LFC (log fold change)
- w scores
- std err
- p-vals
- q-vals
Unit test suite and usage examples for ancombc method

lizgehret commented 1 year ago

Moving this to an active PR, but this is still in development. Once unit test suite is finished, this will be ready for review.

lizgehret commented 1 year ago

Alright @ebolyen I think this one's ready for a semi-final review. Only thing that remains to be finished is:

One test confirming the level ordering behavior

And of course anything else that I may have missed!

Oddant1 commented 1 year ago

Hmm turns out I don't know how to select an entire block of code to show in the preview window thing on the comment. Hopefully, it's obvious what I'm talking about anyway.