summary.scantwoperm {qtl}R Documentation

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.

Details

We take the 1-alpha quantiles of the individual LOD scores.

Value

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

Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

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)

operm <- scantwo(fake.f2, n.perm=100, method="hk")
summary(operm)
[Package qtl version 1.11-12 Index]