table of contents
other versions
- bullseye 1.0.8-3
| RUN_LEFSE(1) | User Commands | RUN_LEFSE(1) |
NAME¶
run_lefse - determine features of organisms, clades, taxonomic units, genes
SYNOPSIS¶
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
DESCRIPTION¶
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)
AUTHOR¶
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 |