Specify an alpha level for computing comparison-wise and experiment-wise critical values for the LOD scores based on the permutation test statistics .
• Comparison wise critical LOD values are computed at each QTL testing point by computing the 100(1- alpha )% percentile from the N LOD scores obtained from the permutation analysis (where N is the number of permutations performed).
• Experiment wise critical LOD thresholds are computed by finding the maximum LOD scores over all QTL testing points for each of the N permutation analyses. The 100(1- alpha )% percentile of these values for each trait is reported as the experimentwise critical LOD thresholds and are drawn on the LOD score plots.Exact p-values for the LOD scores (calculated based on the empirical distribution ) are also reported using the alpha specified here as a reference significance threshold.To Specify an Alpha Level:
Churchill, G.A., and R.W. Doerge. 1994. Empirical threshold values for quantitative trait mapping. Genetics 138:963-971.