Reference: So H.C. and Sham P.C. Robust association tests under different genetic models, allowing for binary or quantitative traits and covariates. Behavior Genetics. Pubished online 9th Feb 2011. pdf
The R packages and pdf manual are attached below.
Instructions:
Please type the following commands before loading the package
Updated Mar 2017
We note that snpStats has replaced snpMatrix so please follow the instructions below
1) installing snpStats first from bioconductor; also install car and mvtnorm
source("https://bioconductor.org/biocLite.R") biocLite("snpStats")
install.packages( c("car","mvtnorm") )
2) run source("Combine_all_4_func_TIDY_CORRECTED_snpStats.r")
3) then run the program as per the manual