It suggests a LOD Score for declaring statistical significance for two-point tests for linkage between all pairs of markers, considering that multiple tests are being performed.
suggest.lod(x)an object of class onemap
the suggested LOD to be used for testing linkage
In a somehow naive approach, the function calculates the number of two-point tests that will be performed for all markers in the data set, and then using this to calculate the global alpha required to control type I error using Bonferroni's correction.
From this global alpha, the corresponding quantile from the chi-square distribution is taken and then converted to LOD Score.
This can be seen as just an initial approximation to help users to select a LOD Score for two point tests.