Powerful Identification of Large Quantitative Trait Loci Using Genome-Wide R/glmnet-Based Regression

R/glmnet has been successfully applied to jointly mapped multiple quantitative trait loci for linkage analysis, along with statistical inference for quantitative trait loci candidates with nonzero genetic effects using R/lm for normally distributed traits, R/glm for discrete traits, and R/coxph for survival times. In this study, we extended R/glmnet to a genome-wide association study by means of parallel computation. A multi-locus genome-wide association study for high-throughput single-nucleotide polymorphisms was implemented in the "Multi-Runking" software written within the R workspace. This software can better detect common and large quantitative trait nucleotides and more accurately estimate than genome-wide mixed model analysis for one single-nucleotide polymorphism at a time and linear mixed models-least absolute shrinkage and selection operator. Its applicability and utility were demonstrated by multi-locus genome-wide association studies for the simulated and real traits distributed normally, binary traits, and survival times.