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Linear discriminant analysis Effect Size (LEfSe) [13]

ZW Zachary D. Wallen
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Genera counts were transformed using TSS. Sample IDs, case/control class designations, and genera relative abundances were exported from R and used as input for LEfSe v 1.0.8.post1 (downloaded using LEfSe bioconda recipe https://bioconda.github.io/recipes/lefse/README.html). Only genus level taxonomy designations were included in the LEfSe input. The LEfSe input was formatted using the lefse-format_input.py script specifying the normalization value to be “1E6”. LEfSe analysis was then ran on the formatted data using the run_lefse.py script with default parameters. Since LEfSe only outputs uncorrected P values for features that it finds significant, LEfSe analysis was ran again, but this time specifying parameters that would output all P values. The full range of LEfSe P values were multiple testing corrected using BH FDR method implemented in the p.adjust function from stats package. These corrected P values were substituted for the uncorrected P values outputted by the default LEfSe run.

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