R: Bayesian credible interval

bayesint {qtl} | R Documentation

## 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)

### 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.

### 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.

### Value

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

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`scanone`, `lodint`

### Examples

    data(hyper)

    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)

[Package qtl version 1.41-6 Index]