allelic.exact.test {allelic} | R Documentation |
This is the implementation in R+C of a new association test described in "A fast, unbiased and exact allelic exact test for case-control association studies" (Submitted). It appears that in most cases the classical chi-square test used for testing for allelic association on genotype data is biased. Our test is unbiased, exact but fast throught careful optimization.
allelic.exact.test(d0,d1,d2,h0,h1,h2)
Takes the 2x3 contingency table on which to compute the test
aa | aA | AA | |
[case (diseased)] | d0 | d1 | d2 |
[control(healthy)] | h0 | h1 | h2 |
d0 |
nb of first homozygous among cases |
d1 |
nb of heterozygous among cases |
d2 |
nb of second homozygous among cases |
h0 |
nb of first homozygous among controls |
h1 |
nb of heterozygous among controls |
h2 |
nb of second homozygous among controls |
return the p-value of the test, or -1 if the sum of all cells in table is greater than TABLE\_OF\_LOG\_FACTORIALS\_SIZE, a C symbol defined in src/newallelic.c
allelic.exact.test(160,80,60,160,160,30)