R: Plot LOD*Effect curves of a multiple-QTL model

mqmplot.directedqtl {qtl} | R Documentation

## Plot LOD*Effect curves of a multiple-QTL model

### Description

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

### Usage

    mqmplot.directedqtl(cross, mqmresult, pheno.col=1, draw = TRUE)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`mqmresult` | Results from mqmscan of type `scanone`
`pheno.col` | From which phenotype in the crossobject are the result calculated
`draw` | If TRUE, draw the figure.

### Value

Returns a scanone object, with added the effectsign calculated internally by the function effect.scan. For more info on the scanone object see: `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 <- fill.geno(f2cross)                           # Fill in missing genotypes
    f2result <- mqmscan(f2cross)                        # Do a MQM scan of the genome
    mqmplot.directedqtl(f2cross,f2result)

[Package qtl version 1.46-2 Index]