calculate_p_values - CLI interface

Calculate p-values for observed data compared with random.

calculate_p_values [-h] [--config_file CONFIG_FILE] [-m {bonferroni,fdr,raw}]
                   [--num_permutations NUM_PERMUTATIONS] [--abs] [--alpha ALPHA]
                   [-s SIGNIFICANCE_MATRIX_FILENAME]
                   p_values_matrix observed_matrix random_matrix [random_matrix ...]

calculate_p_values positional arguments

p_values_matrix - Path to write the computed p-values matrix. (default: None)
observed_matrix - Path to the observed data matrix. (default: None)
random_matrix - Path to the random data matrix. (default: None)

calculate_p_values optional arguments

-h, --help - show this help message and exit
--config_file CONFIG_FILE - Path to configuration file. (default: None)
-m SIGNIFICANCE_METHOD, --significance_method SIGNIFICANCE_METHOD - If provided, correct the p-values using the Bonferroni method (bonferroni)or Benjamini and Hochberg method (fdr). (default: raw)
--num_permutations NUM_PERMUTATIONS, -n NUM_PERMUTATIONS - The total number of random iterations used (useful if only computingp-values for a subset of randomizations). (default: None)
--abs - Compare absolute values instead of signed values.
--alpha ALPHA - Alpha value for statistical significance or False Discovery Rate. (default: 0.05)
-s SIGNIFICANCE_MATRIX_FILENAME, --significance_matrix_filename SIGNIFICANCE_MATRIX_FILENAME - Path to write significance matrix. (default: None)