Compute mutation probabilities

The weighted exclusivity test requires per gene, per patient/sample mutation probabilities as input. We estimate these probabilities directly from permutations of the mutation matrix A where we fix both the row sums (i.e. gene mutation frequencies) and column sums (i.e. patient mutation frequencies). To do so, we use the script compute_mutation_probabilities.py, whose arguments we describe in detail here. You can choose to output just the mutation probabilities (--weights_file), the permuted matrices (in --permutation_directory), or both.

Arguments

Argument	Required (Default)	Description
-mf/--mutation_file	True	Path to mutation file generated by process_mutations.py.
-pd/--permutation_directory	False	Path to permuted mutation matrix files generated by permute_matrix.py.
-wf/--weights_file	False	Path to output file in numpy binary format.
-np/--num_permutations	True	Number of permutations to use when computing mutation probabilities.
-nc/--num_cores	False (1)	Number of cores to utlilize using multiprocessing.
-h/--help	False	Display usage instructions.
-s/--seed	False (Random seed)	Random seed for permuted mutation matrices.
-v/--verbose	False (0)	Choices: 0, 1, 2, 3, 4, 5. Higher values correspond to more verbose output.

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Last modified: 1:43 PM Tuesday, Jan 2, 2017 (EST)