R: Plot results from mqmpermutation

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` | `mqmmulti` object returned by `mqmpermutation` permutation analysis.
`...` | Extra arguments passed to `polyplot`

### Value

No value returned (plotting routine)

### Author(s)

Danny Arends danny.arends@gmail.com , Rutger Brouwer

### See Also

- 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

### 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 1.41-6 Index]