mqmplotpermutations: Plot results from mqmpermutation

In qtl: Tools for Analyzing QTL Experiments

Plot results from mqmpermutation

Description

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

Usage

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 [e-mail] , Rutger Brouwer

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
# 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)

qtl documentation built on Sept. 11, 2024, 5:43 p.m.