Plot results from mqmpermutation
Plotting routine to display the results from a permutation QTL scan. (the
output of mqmpermutation)
mqmplot.permutations(permutationresult, ...)
permutationresult |
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... |
Extra arguments passed to |
No value returned (plotting routine)
Danny Arends danny.arends@gmail.com , Rutger Brouwer
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
# 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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