qtl (version 1.66)

mqmautocofactors: Automatic setting of cofactors, taking marker density into account

Description

Sets cofactors, taking underlying marker density into account. Together with mqmscan cofactors are selected through backward elimination.

Usage

mqmautocofactors(cross, num=50, distance=5, dominance=FALSE, plot=FALSE, verbose=FALSE)

Value

A list of cofactors to be used with mqmscan.

Arguments

cross

An object of class cross. See read.cross for details.

num

Number of cofactors to set (warns when setting too many cofactors).

distance

Minimal distance between two cofactors, in cM.

dominance

If TRUE, create a cofactor list that is safe to use with the dominance scan mode of MQM. See mqmscan for details.

plot

If TRUE, plots a genetic map displaying the selected markers as cofactors.

verbose

If TRUE, give verbose output.

Author

Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman

See Also

• 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

Examples

    data(hyper)                     # hyper dataset
    hyper <- hyper[1:5]
    hyperfilled <- fill.geno(hyper)
    cofactors <- mqmautocofactors(hyperfilled,15)	# Set 15 Cofactors
    result <- mqmscan(hyperfilled,cofactors)	# Backward model selection
    mqmgetmodel(result)