comet_exact_test {cometExactTest}

CoMEt exact test for 2^k contingency tables

Description

This function performs the CoMEt exact test for a given 2^k contingency table.

Usage

comet_exact_test(tbl, pvalthresh=1.1, mutmatplot=T)

Arguments

tbl

is a vector of 2^k non-negative integers (where k is the number of dimensions in your contingency table). We represent each cell of the contingency table as a binary string, and the order of values in the table follows the Least Significant Bit for the binary representation of a given cell. The binary representation for the 2x2 contingency table X for a pair of genes is x00, x01, x10, x11, where x00 is the cell where neither gene is mutated, x01 is the cell where the first gene is mutated and the second is not, etc. Take the following 2x2x2 contingency table as an additional example, where the ordering of the vector is x000, x001, x010, x011, x100, x101, x110, x111.

pvalthresh

is a float specifying the threshold at which the cometexacttest will halt execution if the P-value being computed is ever more than the threshold.

mutmatplot

is a boolean specifying to create mutation matrix of the input table or not. If mutmatplot==T, a file "cometExactTest_plot.pdf" will be created under your working directory.

Examples

  comet_exact_test(c(33, 10, 10, 1, 10, 0, 0, 1))  # 2^3 test => 0.02303503