qtl: lodint – R documentation

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Documentation

qtl

lodint

LOD support interval

Description

Calculate a LOD support interval for a particular chromosome, using output from scanone.

Usage

lodint(results, chr, qtl.index, drop=1.5, 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).
`drop`	LOD units to drop to form 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.

Value

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

Author(s)

Karl W Broman, broman@wisc.edu

Examples

data(hyper)

hyper <- calc.genoprob(hyper, step=0.5)
out <- scanone(hyper, method="hk")
lodint(out, chr=1)
lodint(out, chr=4)
lodint(out, chr=4, drop=2)
lodint(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