qtl (version 1.21-2)

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 class 'scantwoperm':
summary(object, alpha=c(0.05, 0.10), df=FALSE, ...)

Arguments

object

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

alpha

Genome-wide significance levels.

df

If TRUE, the degrees of freedom associated with the LOD scores are shown.

...

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.

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

operm <- scantwo(fake.f2, n.perm=100, method="hk")
summary(operm)