R: Plot LOD curves of a multiple-QTL model

mqmplot.singletrait {qtl} | R Documentation

## Plot LOD curves of a multiple-QTL model

### Description

Plot the LOD curve for a genome scan for a single trait, with a multiple-QTL model (the output of `mqmscan`).

### Usage

    mqmplot.singletrait(result, extended = 0 ,...)

### Arguments

`result` | `mqmscan` result.
`extended` | Extended plotting of the information content
`...` | Extra arguments passed to `plot.scanone`

### Author(s)

Danny Arends danny.arends@gmail.com

### 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 <- mqmaugment(f2cross)
    f2result <- mqmscan(f2cross)                        # Do a MQM scan of the genome
    mqmplot.singletrait(f2result)					# Use our fancy plotting routine

[Package qtl version 1.46-2 Index]