qtl (version 1.66)

mqmplot.directedqtl: Plot LOD*Effect curves of a multiple-QTL model

Description

Plot the LOD*Effect curve for a genome scan with a multiple-QTL model (the output of mqmscan).

Usage

mqmplot.directedqtl(cross, mqmresult, pheno.col=1, draw = TRUE)

Value

Returns a scanone object, with added the effectsign calculated internally by the function effect.scan. For more info on the scanone object see: scanone

Arguments

cross

An object of class cross. See read.cross for details.

mqmresult

Results from mqmscan of type scanone

pheno.col

From which phenotype in the crossobject are the result calculated

draw

If TRUE, draw the figure.

Author

Danny Arends

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
f2qtl <- c(3,15,1,0)                                    # QTL at chromosome 3
data(map10)                                             # Mouse genetic map
map10 <- map10[1:3]
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)