Retrieve the QTL model used in mapping from the results of an MQM scan
Retrieves the QTL model used for scanning from the output of an MQM scan. The model only contains the selected cofactors significant at the specified cofactor.significance from the results of an mqm scan
mqmgetmodel(scanresult)
scanresult |
An object returned by |
The function returns the multiple QTL model created, which consists of the cofactors selected during the modeling phase of the algorithm.
This model was used when scanning for additional QTL in the mqmscan function. The format of the model is compatible with the
makeqtl function. For more information about the format of the model see the makeqtl page.
When no cofactor was selected in the modeling phase no model was created, then this function will return a NULL value.
Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman broman@wisc.edu
mqmsetcofactors - Setting multiple cofactors for backward elimination
makeqtl - Make a qtl object
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)
hyperfilled <- fill.geno(hyper)
cofactors <- mqmsetcofactors(hyperfilled,4)
result <- mqmscan(hyperfilled,cofactors)
mqmgetmodel(result)
plot(mqmgetmodel(result))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.