mqmplotdirectedqtl: Plot LOD*Effect curves of a multiple-QTL model

In kbroman/qtl: Tools for Analyzing QTL Experiments

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)

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.

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

Author(s)

Danny Arends [e-mail]

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

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)

kbroman/qtl documentation built on Jan. 13, 2024, 10:14 p.m.