Permutation Tests

The -r option tells LRmapqtl to perform a permutation test [Churchill and DoergeChurchill and Doerge1994]. The argument to -r indicates how many permutations should be performed. In each permutation, the phenotypes are shuffled relative to the genotypes over individuals and the analysis is redone. The results are summarized at the end of the LRmapqtl output file.