Plot LOD*Effect curves of a multiple-QTL model
Plot the LOD*Effect curve for a genome scan with a multiple-QTL model (the
output of mqmscan).
mqmplot.directedqtl(cross, mqmresult, pheno.col=1, draw = TRUE)
cross |
An object of class |
mqmresult |
Results from mqmscan of type |
pheno.col |
From which phenotype in the crossobject are the result calculated |
draw |
If TRUE, draw the figure. |
Returns a scanone object, with added the effectsign calculated
internally by the function effect.scan. For more info on the
scanone object see: scanone
Danny Arends danny.arends@gmail.com
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 f2qtl <- c(3,15,1,0) # QTL at chromosome 3 data(map10) # Mouse genetic map f2cross <- sim.cross(map10,f2qtl,n=100,type="f2") # Simulate a F2 Cross f2cross <- fill.geno(f2cross) # Fill in missing genotypes f2result <- mqmscan(f2cross) # Do a MQM scan of the genome mqmplot.directedqtl(f2cross,f2result)
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