run_lefse1

Determine features of organisms, clades, taxonomic units, genes

Usage

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

Overview

LEfSe 1.0

Options

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: whether 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 independent 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)