qtl (version 1.41-6)

mqmplot.permutations: Plot results from mqmpermutation

Description

Plotting routine to display the results from a permutation QTL scan. (the output of mqmpermutation)

Usage

mqmplot.permutations(permutationresult, …)

Arguments

permutationresult

mqmmulti object returned by mqmpermutation permutation analysis.

…

Extra arguments passed to polyplot

Value

No value returned (plotting routine)

See Also

• The MQM tutorial: http://www.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
# QTL at chromosome 3
f2qtl <- c(3,15,1,0)

# Mouse genetic map
data(map10)


# Simulate a F2 Cross
f2cross <- sim.cross(map10,f2qtl,n=100,type="f2")
f2cross <- calc.genoprob(f2cross)
# Permutations to obtain significance threshold
f2result <- mqmpermutation(f2cross, n.perm=1000, method="permutation")


# Plot results
mqmplot.permutations(f2result)