Suggests a LOD Score for two point tests
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)
x: an object of class sequence or onemapthe 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.
data(onemap_example_bc) # Loads a fake backcross dataset installed with onemap suggest_lod(onemap_example_bc) # An value that should be used to start the analysis
Useful links