qtl: bayesint – R documentation

Pricing

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

Get Started for Free

Documentation

qtl

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)

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, broman@wisc.edu

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)

qtl

Tools for Analyzing QTL Experiments

v1.48-1

GPL-3

Authors

Karl W Broman <broman@wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, Brian Yandell, and R Core Team

Initial release

2021-03-24