How to set LDA score cutoff and Kruskal-Wallis p-value cutoff?

[lwaldron]

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]

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

#' @param kw.threshold
#' @param wilcoxon.threshold

[lwaldron]

Document how to set a LDA effect size threshold?

[asyakhl]

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