LEFSE_RUN.PY

NAME

lefse_run.py - determine features of organisms, clades, taxonomic units, genes

DESCRIPTION

usage: lefse_run.py [-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 1.1.01

positional arguments:

INPUT_FILE

the input file

OUTPUT_FILE

the output file containing the data for the visualization module

optional arguments:

-h, --help

show this help message and exit

-o str

set the file for exporting the result (only concise textual form)

-a float

set the alpha value for the Anova test (default 0.05)

-w float

set the alpha value for the Wilcoxon test (default 0.05)

-l float

set the threshold on the absolute value of the logarithmic LDA score (default 2.0)

--nlogs int

max log ingluence of LDA coeff

--verbose int

verbose execution (default 0)

--wilc int

wheter to perform the Wicoxon step (default 1)

-r str

select LDA or SVM for effect size (default LDA)

--svm_norm int

whether to normalize the data in [0,1] for SVM feature waiting (default 1 strongly suggested)

-b int

set the number of bootstrap iteration for LDA (default 30)

-e int

set whether perform the wilcoxon test only among the subclasses with the same name (default 0)

-c int

set whether perform the wilcoxon test ing the Curtis’s approach [BETA VERSION] (default 0)

-f float

set the subsampling fraction value for each bootstrap iteration (default 0.66666)

-s {0,1,2}

set the multiple testing correction options. 0 no correction (more strict, default), 1 correction for independent comparisons, 2 correction for dependent comparison

--min_c int

minimum number of samples per subclass for performing wilcoxon test (default 10)

-t str

set the title of the analysis (default input file without extension)

-y {0,1}

(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)

AUTHOR

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