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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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getPrevalence defaults #377

Closed antagomir closed 1 year ago

antagomir commented 1 year ago

The getPrevalence argument as_relative=TRUE by default.

I realized that this can be confusing when calling the function with "counts" assay, and having it to change the behavior to as_relative by default. This would also be a problem if something else than counts (e.g. log10) would be used as the starting assay.

I suggest to change the default to as_relative=FALSE in all prevalence functions (getPrevalence, getPrevalent* etc.)

antagomir commented 1 year ago

After changing also check that OMA explanations will still be correct with respect to the new default. Perhaps no need for changes but needs to be checked.