Set cofactors at fixed intervals, to be used with MQM
Set cofactors, at fixed marker intervals. Together
with mqmscan cofactors are selected through backward elimination.
mqmsetcofactors(cross, each = NULL, cofactors=NULL, sexfactors=NULL, verbose=FALSE)
cross |
An object of class |
each |
Every 'each' marker will be used as a cofactor, when each is used the |
cofactors |
List of cofactors to be analysed in the QTL model. To set cofactors use |
sexfactors |
list of markers which should be treated as dominant cofactors (sexfactors), when |
verbose |
If TRUE, print tracing information. |
An list of cofactors to be passed into mqmscan.
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
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.