mqmgetmodel: Retrieve the QTL model used in mapping from the results of an...
In byandell/qtl: Tools for analyzing QTL experiments

Description Usage Arguments Value Author(s) See Also Examples

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

1	mqmgetmodel(scanresult)

scanresult

An object returned by mqmscan, including cofactors and QTL model.

The function returns the QTL model created (cofactors selected in modeling found to be significant at cofactor.significance) and used during the mqmscan See for the format of the model: makeqtl returns NULL when no cofactors reach the significance threshold during QTL modeling.

Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman kbroman@biostat.wisc.edu

mqmsetcofactors - Setting multiple cofactors for backward elimination
makeqtl - Make a qtl object
The MQM tutorial: http://www.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))