qtl (version 1.66)

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, ...)

Value

No value returned (plotting routine)

Arguments

permutationresult

mqmmulti object returned by mqmpermutation permutation analysis.

...

Extra arguments passed to polyplot

Author

Danny Arends , Rutger Brouwer

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
# QTL at chromosome 3
f2qtl <- c(3,15,1,0)

# Mouse genetic map
data(map10)

map10 <- map10[1:3]
# Simulate a F2 Cross
f2cross <- sim.cross(map10,f2qtl,n=100,type="f2")
f2cross <- calc.genoprob(f2cross)
if (FALSE) # Permutations to obtain significance threshold
f2result <- mqmpermutation(f2cross, n.perm=1000, method="permutation")
f2result <- mqmpermutation(f2cross, n.perm=2, batchsize=2, method="permutation")

# Plot results
mqmplot.permutations(f2result)