qtl (version 1.70)

bayesint: Bayesian credible interval

Description

Calculate an approximate Bayesian credible interval for a particular chromosome, using output from scanone.

Usage

bayesint(results, chr, qtl.index, prob=0.95, lodcolumn=1, expandtomarkers=FALSE)

Value

An object of class scanone indicating the estimated QTL position and the approximate endpoints for the Bayesian credible interval.

Arguments

results

Output from scanone, or a qtl object as output from refineqtl.

chr

A chromosome ID (if input results are from scanone (should have length 1).

qtl.index

Numeric index for a QTL (if input results are from refineqtl (should have length 1).

prob

Probability coverage of the interval.

lodcolumn

An integer indicating which of the LOD score columns should be considered (if input results are from scanone).

expandtomarkers

If TRUE, the interval is expanded to the nearest flanking markers.

Author

Karl W Broman,

Details

We take \(10^{LOD}\), rescale it to have area 1, and then calculate the connected interval with density above some threshold and having coverage matching the target probability.

See Also

scanone, lodint

Examples

data(hyper)
hyper <- subset(hyper, chr=c(1,4))
hyper <- calc.genoprob(hyper, step=0.5)
out <- scanone(hyper, method="hk")
bayesint(out, chr=1)
bayesint(out, chr=4)
bayesint(out, chr=4, prob=0.99)
bayesint(out, chr=4, expandtomarkers=TRUE)