R: Set cofactors at fixed intervals, to be used with MQM

mqmsetcofactors {qtl} | R Documentation

## Set cofactors at fixed intervals, to be used with MQM

### Description

Set cofactors, at fixed marker intervals. Together with `mqmscan` cofactors are selected through backward elimination.

### Usage

    mqmsetcofactors(cross, each = NULL, cofactors=NULL, sexfactors=NULL, verbose=FALSE)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`each` | Every 'each' marker will be used as a cofactor, when each is used the `cofactors` and `sexfactors` parameter is ignored
`cofactors` | List of cofactors to be analysed in the QTL model. To set cofactors use `mqmautocofactors` or `mqmsetcofactors`; when `each` is set, this parameter is ignored
`sexfactors` | list of markers which should be treated as dominant cofactors (sexfactors), when `each` is set, this parameter is ignored
`verbose` | If TRUE, print tracing information.

### Value

An list of cofactors to be passed into `mqmscan`.

### Author(s)

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

### See Also

- 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)							        # Hyper dataset

    	hyperfilled <- fill.geno(hyper)
      # Automatic cofactors every third marker
    	cofactors <- mqmsetcofactors(hyperfilled,3)
    	result <- mqmscan(hyperfilled,cofactors)	# Backward model selection
    	mqmgetmodel(result)
      #Manual cofactors at markers 3,6,9,12,40 and 60
      cofactors <- mqmsetcofactors(hyperfilled,cofactors=c(3,6,9,12,40,60))
    	result <- mqmscan(hyperfilled,cofactors)	# Backward model selection
    	mqmgetmodel(result)

[Package qtl version 1.41-6 Index]