lodint: LOD support interval

In qtl: Tools for Analyzing QTL Experiments

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, [e-mail]

See Also

scanone, bayesint

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 documentation built on Nov. 28, 2023, 1:09 a.m.