R: cis-trans plot

mqmplot.cistrans {qtl} | R Documentation

## cis-trans plot

### Description

Plot results for a genomescan using a multiple-QTL model. With genetic location for the traits it is possible to show cis- and trans- locations, and detect trans-bands

### Usage

    mqmplot.cistrans(result, cross, threshold=5, onlyPEAK=TRUE,
                     highPEAK=FALSE, cisarea=10, pch=22, cex=0.5,
                     verbose=FALSE, ...)

### Arguments

`result` | An object of class `mqmmulti`. See `mqmscanall` for details.
`cross` | An object of class `cross`. See `read.cross` for details.
`threshold` | Threshold value in LOD, Markers that have a LOD score above this threshold are plotted as small squares (see `pch` parameter). The markers with LODscores below this threshold are not visible
`onlyPEAK` | Plot only the peak markers ? (TRUE/FALSE) (Peak markers are markers that have a QTL likelihood above `threshold` and higher than other markers in the same region)
`highPEAK` | Highlight peak markers ? (TRUE/FALSE). When using this option peak markers (the marker with the highest LOD score in a region above the threshold gets an 25% increase in size and is displayed in red)
`cisarea` | Adjust the two green lines around the line y=x
`pch` | What kind of character is used in plotting of the figure (Default: 22, small square)
`cex` | Size of the points plotted (default to 0.5 half of the original size)
`verbose` | If TRUE, give verbose output
`...` | Extra parameters will be passed to points

### Value

Plotting routine, so no return

### 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

    data(multitrait)

    data(locations)
    multiloc <- addloctocross(multitrait,locations)
    multiloc <- calc.genoprob(multiloc)
    results <- scanall(multiloc, method="hk")
    mqmplot.cistrans(results, multiloc, 5, FALSE, TRUE)

[Package qtl version 1.46-2 Index]