cis-trans plot
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
mqmplot.cistrans(result, cross, threshold=5, onlyPEAK=TRUE,
highPEAK=FALSE, cisarea=10, pch=22, cex=0.5,
verbose=FALSE, ...)result |
An object of class |
cross |
An object of class |
threshold |
Threshold value in LOD, Markers that have a
LOD score above this threshold are plotted as small squares
(see |
onlyPEAK |
Plot only the peak markers ? (TRUE/FALSE)
(Peak markers are markers that have a QTL likelihood above
|
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 |
Plotting routine, so no return
Danny Arends danny.arends@gmail.com
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
data(multitrait) data(locations) multiloc <- addloctocross(multitrait,locations) multiloc <- calc.genoprob(multiloc) results <- scanall(multiloc, method="hk") mqmplot.cistrans(results, multiloc, 5, FALSE, TRUE)
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