gLRTH_A {gLRTH} | R Documentation |
The function for the likelihood ratio test for genome-wide association under genetic heterogeneity with genotype frequencies as input values
Description
We consider a binary trait and focus on detecting association with disease at a single locus with two
alleles and
. The likelihood ratio test is based
on a binomial mixture model of
components (
) for diseased cases:
where ,
is the probability mass function for a binomial distribution
,
and
if and only if
.
is the probability
of having the allele of interest on one chromosome for a subgroup of case
.
In particular,
is likely to be quite
large for many of the complex disease with genetic heterogeneity. Note that the LRT-H can
be applied to association studies without the need to know the exact value of
while allowing
.
Usage
gLRTH_A(n0, n1, n2, m0, m1, m2)
Arguments
n0 |
AA genotype frequency in case |
n1 |
Aa genotype frequency in case |
n2 |
aa genotype frequency in case |
m0 |
AA genotype frequency in control |
m1 |
Aa genotype frequency in control |
m2 |
aa genotype frequency in control |
Value
The test statistic and asymptotic p-value for the likelihood ratio test for GWAS under genetic heterogeneity
Author(s)
Xiaoxia Han and Yongzhao Shao
References
Qian M., Shao Y. (2013) A Likelihood Ratio Test for Genome-Wide Association under Genetic Heterogeneity. Annals of Human Genetics, 77(2): 174-182.
Examples
gLRTH_A(n0=2940, n1=738, n2=53, m0=3601, m1=1173, m2=117)