Output genotype LS means and diffs

Check this box to create a data set containing the LS meansand 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.

To Specify This Option:

8

Ensure that Genotype is selected as one of the Association Tests.

8

Click within the check box.