R: Add phenotype location into a cross object

addloctocross {qtl} | R Documentation

## Add phenotype location into a cross object

### Description

Add phenotype location(s) into a cross object (with eQTL/pQTL studies)

### Usage

    	addloctocross(cross, locations=NULL, locfile="locations.txt", verbose=FALSE)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`locations` | R variable holding location information
`locfile` | load from a file, see the details section for the layout of the file.
`verbose` | If TRUE, give verbose output

### Details

inputfile layout: Num Name Chr cM 1 X3.Hydroxypropyl 4 50.0 Num is the number of the phenotype in the cross object Name is the name of the phenotype (will be checked against the name already in the cross object at position num Chr Chromosome cM postion from start of chromosome in cM

### Value

The input cross object, with the locations added as an aditional component `locations`

### Author(s)

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

### See Also

- `mqmplot.cistrans` - Cis/trans plot

- 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

    ## Not run:
    	data(multitrait)
    	data(locations)
    	multiloc <- addloctocross(multitrait,locations)
    	results <- scanall(multiloc)
    	mqmplot.cistrans(results, multiloc, 5, FALSE, TRUE)

    ## End(Not run)

[Package qtl version 1.41-6 Index]