Plot results from mqmpermutation

Description

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

Usage

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mqmplot.permutations(permutationresult, ...)

Arguments

permutationresult

mqmmulti object returned by mqmpermutation permutation analysis.

...

Extra arguments passed to polyplot

Value

No value returned (plotting routine)

Author(s)

Danny Arends danny.arends@gmail.com , Rutger Brouwer

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

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# 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)

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