summary.scantwoperm: LOD thresholds from scantwo permutation results

In byandell/qtl: Tools for analyzing QTL experiments

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, [e-mail]

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)

byandell/qtl documentation built on May 13, 2019, 9:28 a.m.