qtl (version 1.39-5)

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

"summary"(object, alpha=c(0.05, 0.10), ...)

Arguments

object

Output from the function scantwo with n.perm > 0.

alpha

Genome-wide significance levels.

...

Ignored at this point.

Value

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. Genetics 138, 963--971.

See Also

scantwo, summary.scantwo, plot.scantwoperm

Examples

data(fake.f2)

fake.f2 <- calc.genoprob(fake.f2, step=0)

## Not run: operm <- scantwo(fake.f2, n.perm=100, method="hk")
summary(operm)