The PathScan package is implemented strictly as a test of a set of genes, e.g. a pathway, for a single individual. Specifically, knowing the gene lengths in the pathway, the number of genes that have at least one mutation, and the estimated background mutation rate, one can test the null hypothesis that these observed mutations are well-explained simply by the mechanism of random background mutation. However, it will often be the case that data for a pathway will be available for many individuals, meaning that we now have many tests of the given (single) hypothesis. (This should not be confused with the scenario of multiple hypothesis testing.) The set of values contains much more information than a single value, suggesting that significance must be judged on the basis of the collective result. For example, while no single p-value by itself may exceed the chosen statistical threshold, the overall set of probabilities may still give the impression of significance. Properly combining such numbers is a necessary, but not entirely trivial task. This package basically serves as a high-level interface to first perform individual tests using the methods of PathScan, and then to properly combine the resulting p-values using the methods of CombinePvals.
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Wendl MC, Wallis JW, Lin L, Kandoth C, Mardis ER, Wilson RK, Ding L.
PathScan: A Tool for Discerning Mutational Significance in Groups of Putative Cancer Genes.
Bioinformatics. 2011 Jun 15;27(12):1595-602. Epub 2011 Apr 14