qtl (version 1.39-5)

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

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)
## Not run: # Permutations to obtain significance threshold
# f2result <- mqmpermutation(f2cross, n.perm=1000, method="permutation")
# ## End(Not run)

# Plot results
mqmplot.permutations(f2result)