We developed a weighted exact test for mutually exclusive mutations, which conditions on the number of mutations in each gene and uses per gene, per sample mutation probabilities. We call this a weighted-row exclusivity (WR-exclusivity) test, because it conditions on the number of mutations per gene (row sums of mutation matrix) and uses per gene, per sample weights.
We use our WR-exclusivity test to approximate the row-column exclusivity (RC-exclusivity) test that conditions on the number of mutations per gene and per patient, but is too expensive computationally to compute exactly.
We use our Weighted Exclusivity Test (WExT) software to compute the WR-exclusivity test, either exactly or with a saddlepoint approximation. The software and source code is hosted on GitHub: Source code | Downloads.
Mark D.M. Leiserson, Matthew A. Reyna, Benjamin J. Raphael. (2016) A Weighted Exact Test for Mutually Exclusive Mutations in Cancer. ECCB/Bioinformatics (to appear). arXiv preprint