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waldronlab / lefser

R implementation of the LEfSe method
https://waldronlab.io/lefser/
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How to set LDA score cutoff and Kruskal-Wallis p-value cutoff? #8

Closed lwaldron closed 2 months ago

lwaldron commented 3 years ago

Analyses using LEfSE usually state an LDA score cutoff and a Kruskal-Wallis p-value cutoff. I can see how the LDA score cutoff is possible through manual filtering of the lefserAnalysis output, but can't see how to do it for p-value.

Document how to adjust these thresholds in the vignette.

lwaldron commented 3 years ago

Document in https://github.com/waldronlab/lefser/blob/master/R/lefserAnalysis.R:

#' @param kw.threshold
#' @param wilcoxon.threshold
lwaldron commented 3 years ago

Document how to set a LDA effect size threshold?

asyakhl commented 3 years ago

I had added the LDA cutoff, I created a branch for that.