qtl (version 1.66)

mqmplot.singletrait: Plot LOD curves of a multiple-QTL model

Description

Plot the LOD curve for a genome scan for a single trait, with a multiple-QTL model (the output of mqmscan).

Usage

mqmplot.singletrait(result, extended = 0 ,...)

Arguments

result

mqmscan result.

extended

Extended plotting of the information content

...

Extra arguments passed to plot.scanone

Author

Danny Arends

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

#Simulated F2 Population
f2qtl <- c(3,15,1,0)                                    # QTL at chromosome 3
data(map10)                                             # Mouse genetic map
map10 <- map10[1:3]
f2cross <- sim.cross(map10,f2qtl,n=100,type="f2")       # Simulate a F2 Cross
f2cross <- mqmaugment(f2cross)
f2result <- mqmscan(f2cross)                        # Do a MQM scan of the genome
mqmplot.singletrait(f2result)					# Use our fancy plotting routine