R: Plot cofactors on the genetic map

mqmplot.cofactors {qtl} | R Documentation

## Plot cofactors on the genetic map

### Description

Plots cofactors as created by `mqmsetcofactors` or `mqmautocofactors` on the genetic map.

### Usage

    mqmplot.cofactors(cross,cofactors, ...)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`cofactors` | List of cofactors to be analysed in the QTL model. To set cofactors use `mqmautocofactors` or `mqmsetcofactors`

.

`...` | Passed to `plot.qtl`

### 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

    data(multitrait)
    cof1 <- mqmsetcofactors(multitrait,20)
    cof2 <- mqmsetcofactors(multitrait,10)
    op <- par(mfrow=c(2,1))
    mqmplot.cofactors(multitrait,cof1,col="blue")
    mqmplot.cofactors(multitrait,cof2,col="blue")
    op <- par(mfrow=c(1,1))

[Package qtl version 1.46-2 Index]