R: Retrieve the QTL model used in mapping from the results of an...

mqmgetmodel {qtl} | R Documentation

## Retrieve the QTL model used in mapping from the results of an MQM scan

### Description

Retrieves the QTL model used for scanning from the output of an MQM scan. The model only contains the selected cofactors significant at the specified cofactor.significance from the results of an mqm scan

### Usage

    	mqmgetmodel(scanresult)

### Arguments

`scanresult` | An object returned by `mqmscan`, including cofactors and QTL model.

### Value

The function returns the QTL model created (cofactors selected in modeling found to be significant at cofactor.significance) and used during the mqmscan See for the format of the model: `makeqtl` returns NULL when no cofactors reach the significance threshold during QTL modeling.

### Author(s)

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

### See Also

- `mqmsetcofactors` - Setting multiple cofactors for backward elimination

- `makeqtl` - Make a qtl object

- 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

    	data(hyper)

    	hyperfilled <- fill.geno(hyper)
    	cofactors <- mqmsetcofactors(hyperfilled,4)
    	result <- mqmscan(hyperfilled,cofactors)
    	mqmgetmodel(result)
    	plot(mqmgetmodel(result))

[Package qtl version 1.41-6 Index]