Thresholds derived from scantwo
permutations (that
is, for a two-dimensional, two-QTL genome scan) are used to calculate
penalties on main effects and interactions.
The main effect penalty is the 1-alpha
quantile of the null
distribution of the genome-wide maximum LOD score from a single-QTL
genome scan (as with scanone
).
The "heavy" interaction penalty is the 1-alpha
quantile of
the null distribution of the maximum interaction LOD score (that is,
the \(\log_{10}\) likelihood ratio comparing the best model
with two interacting QTL to the best model with two additive QTL) from
a two-dimensional, two-QTL genome scan (as with
scantwo
).
The "light" interaction penality is the difference between the
"fv1"
threshold from the scantwo
permutations (that is, the 1-alpha
quantile of the LOD score
comparing the best model with two interacting QTL to the best
single-QTL model) and the main effect penalty.
If the permutations results were obtained with perm.Xsp=TRUE
,
to give X-chr-specific results, six penalties are calculated: main
effect for autosomes, main effect for X chr, heavy penalty on A:A
interactions, light penalty on A:A interactions, penalty on A:X
interactions, and penalty on X:X interactions.