qtl (version 1.38-4)

mqmplot.permutations: 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)

See Also

% \input{"inst/docs/Sources/MQM/mqm/standard_seealso.txt"}
• The MQM tutorial:http://www.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 % -----^^ inst/docs/Sources/MQM/mqm/standard_seealso.txt ^^-----

Examples

# Simulated F2 Population
# QTL at chromosome 3
f2qtl <- c(3,15,1,0)

# Mouse genetic map
data(map10)

map10 <- map10[1:3]
# Simulate a F2 Cross
f2cross <- sim.cross(map10,f2qtl,n=100,type="f2")
f2cross <- calc.genoprob(f2cross)
# Permutations to obtain significance threshold
f2result <- mqmpermutation(f2cross, n.perm=1000, method="permutation")f2result <- mqmpermutation(f2cross, n.perm=2, batchsize=2, method="permutation")

# Plot results
mqmplot.permutations(f2result)