mqmplot.cofactors {qtl}

Plot cofactors on the genetic map

Description

Plots cofactors as created by mqmsetcofactors or mqmautocofactors on the genetic map.

Usage

mqmplot.cofactors(cross,cofactors, ...)

Arguments

cross

An object of class cross. See read.cross for details.

cofactors

List of cofactors to be analysed in the QTL model. To set cofactors use mqmautocofactors or mqmsetcofactors

.

...

Passed to plot.qtl

Author(s)

Danny Arends [e-mail]

See Also

• The MQM tutorial: https://rqtl.org/tutorials/MQM-tour.pdf

• MQM - MQM description and references

• mqmscan - Main MQM single trait analysis

• mqmscanall - Parallellized traits analysis

• mqmaugment - Augmentation routine for estimating missing data

• mqmautocofactors - Set cofactors using marker density

• mqmsetcofactors - Set cofactors at fixed locations

• mqmpermutation - Estimate significance levels

• scanone - Single QTL scanning

Examples

data(multitrait)
cof1 <- mqmsetcofactors(multitrait,20)
cof2 <- mqmsetcofactors(multitrait,10)
op <- par(mfrow=c(2,1))
mqmplot.cofactors(multitrait,cof1,col="blue")
mqmplot.cofactors(multitrait,cof2,col="blue")
op <- par(mfrow=c(1,1))