An object of class summary.scantwoperm, to be printed by
print.summary.scantwoperm.
Details
We take the \(1-\alpha\) quantiles of the individual LOD
scores.
In the case of X-chr-specific permutations, we use the combined length
of the autosomes, \(L_A\), and the length of the X chromosome,
\(L_X\), and calculate the area of the A:A, A:X, and X:X regions as
\(L_A^2/2\), \(L_A L_X\), and \(L_X^2/2\), and then use the
nominal significance levels of \(1 - (1-\alpha)^p\),
where \(p\) is the proportional area for that region.
References
Churchill, G. A. and Doerge, R. W. (1994) Empirical threshold values for
quantitative trait mapping. Genetics138, 963--971.
# NOT RUN {data(fake.f2)
# }# NOT RUN {fake.f2 <- calc.genoprob(fake.f2, step=0)
# }# NOT RUN {operm <- scantwo(fake.f2, n.perm=100, method="hk")
# }# NOT RUN {summary(operm)
# }