mqmplot.permutations {qtl} | R Documentation |
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 |
|
... |
Extra arguments passed to |
Value
No value returned (plotting routine)
Author(s)
Danny Arends danny.arends@gmail.com , 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)
[Package qtl version 1.66 Index]