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 Plot
s 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.
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