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