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FEAT: ANCOM-BC R wrapper #88

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merged 62 commits into from
Oct 21, 2022
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@lizgehret lizgehret commented Jun 27, 2022

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

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@lizgehret lizgehret changed the title FEAT: ANCOM-BC R wrapper script FEAT: ANCOM-BC R wrapper Jul 12, 2022
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lizgehret commented Sep 23, 2022

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!

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@Oddant1 Oddant1 left a comment

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Looks pretty good. Some parts, like the usage examples and the tests, I don't really feel like I can give solid feedback on because I'm not sure exactly what needs to be covered, but it looks like you hit the relevant points.

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Oddant1 commented Oct 13, 2022

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.

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@ebolyen ebolyen left a comment

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Very nicely done @lizgehret. The R code is quite aesthetic relative to most R code out there.

Few very minor comments on the plugin-setup parameter descriptions.

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Thanks @lizgehret!

@ebolyen ebolyen merged commit a6ca6ce into qiime2:ANCOM-wrapper Oct 21, 2022
@lizgehret lizgehret deleted the ancombc-script branch October 21, 2022 18:45
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3 participants