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, broman@wisc.edu

Details

We take $10^{L O D}$ , rescale it to have area 1, and then calculate the connected interval with density above some threshold and having coverage matching the target probability.

Examples

Run this code

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)

Run the code above in your browser using DataLab

Last chance! 50% off unlimited learning