Learn R Programming

qtl (version 1.70)

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 danny.arends@gmail.com

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

Run this code
#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

Run the code above in your browser using DataLab