qtl (version 1.70)

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)

Value

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

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.

Author

Karl W Broman,

See Also

scanone, bayesint

Examples

data(hyper)
hyper <- subset(hyper, chr=c(1,4))
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)