Scroll to navigation

RUN_LEFSE(1) User Commands RUN_LEFSE(1)


run_lefse - determine features of organisms, clades, taxonomic units, genes


run_lefse [-h] [-o str] [-a float] [-w float] [-l float] [--nlogs int] [--verbose int] [--wilc int] [-r str] [--svm_norm int] [-b int] [-e int] [-c int] [-f float] [-s {0,1,2}] [--min_c int] [-t str] [-y {0,1}] INPUT_FILE OUTPUT_FILE


LEfSe 1.0


positional arguments:

the input file
the output file containing the data for the visualization module

optional arguments:

show this help message and exit
set the file for exporting the result (only concise textual form)
set the alpha value for the Anova test (default 0.05)
set the alpha value for the Wilcoxon test (default 0.05)
set the threshold on the absolute value of the logarithmic LDA score (default 2.0)
max log ingluence of LDA coeff
verbose execution (default 0)
whether to perform the Wicoxon step (default 1)
select LDA or SVM for effect size (default LDA)
whether to normalize the data in [0,1] for SVM feature waiting (default 1 strongly suggested)
set the number of bootstrap iteration for LDA (default 30)
set whether perform the wilcoxon test only among the subclasses with the same name (default 0)
set whether perform the wilcoxon test ing the Curtis's approach [BETA VERSION] (default 0)
set the subsampling fraction value for each bootstrap iteration (default 0.66666)
set the multiple testing correction options. 0 no correction (more strict, default), 1 correction for independent comparisons, 2 correction for independent comparison
minimum number of samples per subclass for performing wilcoxon test (default 10)
set the title of the analysis (default input file without extension)
(for multiclass tasks) set whether the test is performed in a one-against-one ( 1 - more strict!) or in a one-againstall setting ( 0 - less strict) (default 0)


This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

September 2019 run_lefse 1.0.8