Abstract
We present vqtl, an R package for mean-variance QTL mapping. This QTL mapping approach tests for genetic loci that influence the mean of the phenotype, termed mean QTL, the variance of the phenotype, termed variance QTL, or some combination of the two, termed mean-variance QTL. It is unique in its ability to correct for variance heterogeneity arising not only from the QTL itself but also from nuisance factors, such as sex, batch, or housing. This package provides functions to conduct genome scans, run permutations to assess the statistical significance, and make informative plots to communicate results. Because it is inter-operable with the popular qtl package and uses many of the same data structures and input patterns, it will be straightforward for geneticists to analyze future experiments with vqtl as well as re-analyze past experiments, possibly discovering new QTL.