Check this box to create a data set containing the LS means and differences for the genotypes when the Genotype test is selected to be performed.
Checking this option in either the SNP-Trait Association or Q-K Mixed Model processes generates Volcano Plots for genotype LS differences and adds two new columns listing the LS differences and associated p-values to the main output data set. Checking this option in the SNP-SNP Interactions process adds four new columns listing the LS differences and associated p-values to the main output data set but does not display the volcano plots.
Note: The LS means and differences from the models that contain Effect-by-SNP interactions are not included.
Note: This option is ignored for Nominal, Ordinal, and Survival traits, and for binary traits when no random effects are specified.
|