nccmo/Permutation-test

Permutation Test

This is a script to identify gens significantly affected by multiple mutations (MMs) using permutation test.

Dependency

python 2.7.15
python packages
annot_utils
pysam (0.14.1)
pandas (0.23.4)
numpy(1.15.3)

Preparation

python lib/permutation_test/preparation2.py
python lib/permutation_test/preparation2.py
python lib/permutation_test/silent.py maf_file

Run

python2 lib/permutation_test/run_simulation.py SNV     maf_file output_file --gene interested_gene
python2 lib/permutation_test/run_simulation.py non_SNV maf_file output_file --gene interested_gene