qtl (version 1.38-4)

mqmgetmodel: Retrieve the QTL model used in mapping from the results of an MQM scan

Description

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

Usage

mqmgetmodel(scanresult)

Arguments

scanresult

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

Value

• 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.

See Also

• mqmsetcofactors- Setting multiple cofactors for backward elimination
• makeqtl- Make a qtl object % \input{"inst/docs/Sources/MQM/mqm/standard_seealso.txt"}
• 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 % -----^^ inst/docs/Sources/MQM/mqm/standard_seealso.txt ^^-----

Examples

data(hyper)
        hyper <- subset(hyper, chr=1:4)
	hyperfilled <- fill.geno(hyper)
	cofactors <- mqmsetcofactors(hyperfilled,4)
	result <- mqmscan(hyperfilled,cofactors)
	mqmgetmodel(result)
	plot(mqmgetmodel(result))