summary.scantwoperm: LOD thresholds from scantwo permutation results

Description

Print the estimated genome-wide LOD thresholds on the basis of permutation results from scantwo (with n.perm > 0).

Usage

# S3 method for scantwoperm
summary(object, alpha=c(0.05, 0.10), ...)

Value

An object of class summary.scantwoperm, to be printed by

print.summary.scantwoperm.

Arguments

object: Output from the function scantwo with n.perm > 0.
alpha: Genome-wide significance levels.
...: Ignored at this point.

Author

Karl W Broman, broman@wisc.edu

Details

We take the $1 - α$ 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 $1 - (1 - α)^{p}$ , 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. Genetics 138, 963--971.

Examples

Run this code

data(fake.f2)
fake.f2 <- subset(fake.f2, chr=c(18:19,"X"), ind=1:50)
fake.f2 <- calc.genoprob(fake.f2, step=0)

if (FALSE) operm <- scantwo(fake.f2, n.perm=100, method="hk")# \dontshow{
operm <- scantwo(fake.f2, n.perm=3, method="hk")# }
summary(operm)

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