Convert mqmmulti objects into a scanoneperm object
Function to convert mqmmulti objects into a scanoneperm
object, this allows the use of R/qtl methods for permutation analysis
that do not support the output of a multiple QTL scan using mqm's
outputstructure.
mqmprocesspermutation(mqmpermutationresult = NULL)
mqmpermutationresult |
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Output of the algorithm is a scanoneperm object. See also: summary.scanoneperm
Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman broman@wisc.edu
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
# QTL at chromosome 3 f2qtl <- c(3,15,1,0) # Mouse genetic map data(map10) # Simulate a F2 Cross f2cross <- sim.cross(map10,f2qtl,n=100,type="f2") ## Not run: # Bootstrap MQM mapping on the f2cross f2result <- mqmpermutation(f2cross,scanfunction=mqmscan) ## End(Not run) # Create a permutation object f2perm <- mqmprocesspermutation(f2result) # What LOD score is considered significant? summary(f2perm)
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