Genetics and population analysis NAM: association studies in multiple populations

Motivation: Mixed linear models provide important techniques for performing genome-wide association studies. However, current models have pitfalls associated with their strong assumptions. Here, we propose a new implementation designed to overcome some of these pitfalls using an empirical Bayes algorithm. Results: Here we introduce NAM, an R package that allows user to take into account prior information regarding population stratification to relax the linkage phase assumption of current methods. It allows markers to be treated as a random effect to increase the resolution, and uses a sliding-window strategy to increase power and avoid double fitting markers into the model. Availability and implementation: NAM is an R package available in the CRAN repository. It can be installed in R by typing install.packages (‘NAM’). Contact: [email protected] Supplementary information: Supplementary date are available at Bioinformatics online.