qtl (version 1.66)

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,

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 <- 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)