| GxEtest {GEVACO} | R Documentation |
Joint test for genetic and gene-environment interaction effects for a single SNP
Description
Function to test for the joint genetic and gene-environment interaction effects for a single variant using a LRT model
Usage
GxEtest(dat, snp_geno, nsim = 1e+05, K)
Arguments
dat |
a data frame with covariate information. Column 1 should be phenotype, column 2 should be the environmental factor of interest, columns 3 and later should be additional covariates |
snp_geno |
a vector containing genotypic information of SNP of interest to be tested |
nsim |
the number of replicates in obtaining the p-value (standard 1e5) |
K |
the number of knots used to control the flexibility in modeling GxE interaction |
Value
empirical p-value obtained as the proportion of T0 that are greater than the observed test statistic T
References
Crainiceanu, C. M., & Ruppert, D. (2004). Likelihood ratio tests in linear mixed models with one variance component. Journal of the Royal Statistical Society Series B-Statistical Methodology, 66, 165-185. doi: 10.1111/j.1467-9868.2004.00438.x