vqtl: An R package for Mean-Variance QTL Mapping

Most existing methods for QTL mapping in experimental crosses assume that the residual variance is constant across all individuals. But common situations violate this assumption. For many phenotypes, one sex is more variable than the other, some experimenters make more precise measurements than others, and specific genetic factors influence environmental sensitivity. In these cases, mean-variance QTL mapping provides higher power and better protection against false positives. It also allows for detection of QTL that influence phenotype variance, termed vQTL. We present R package vqtl. This package makes it easy for geneticists to apply the mean-variance QTL mapping approach, control family-wide error rate (FWER), and visualize and interpret their results. Because this package is interoperable with the popular R/qtl package and uses many of the same data structures and input patterns, it will be easy for geneticists to analyze future experiments with R/vqtl as well as re-analyze past experiments, possibly discovering new QTL.