R: Convert mqmmulti objects into a scanoneperm object

mqmprocesspermutation {qtl} | R Documentation

## Convert mqmmulti objects into a scanoneperm object

### Description

Function to convert `mqmmulti` objects into a `scanoneperm` object, this allows the use of R/qtl methods for permutation analysis that do not support the output of a multiple QTL scan using mqm's outputstructure.

### Usage

    mqmprocesspermutation(mqmpermutationresult = NULL)

### Arguments

`mqmpermutationresult` | `mqmmulti` object obtained after performing permutations on a single trait.using the function `mqmpermutation`

### Value

Output of the algorithm is a `scanoneperm` object. See also: `summary.scanoneperm`

### Author(s)

Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman broman@wisc.edu

### 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

    # 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")
    ## Not run: # Bootstrap MQM mapping on the f2cross
    f2result <- mqmpermutation(f2cross,scanfunction=mqmscan)

    ## End(Not run)

    # Create a permutation object
    f2perm <- mqmprocesspermutation(f2result)

    # What LOD score is considered significant?
    summary(f2perm)

[Package qtl version 1.46-2 Index]