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

In kbroman/qtl: Tools for Analyzing QTL Experiments

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)

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.

Value

A list of cofactors to be used with mqmscan.

Author(s)

Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman [e-mail]

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
    
    hyperfilled <- fill.geno(hyper)
    cofactors <- mqmautocofactors(hyperfilled,15)	# Set 15 Cofactors
    result <- mqmscan(hyperfilled,cofactors)	# Backward model selection
    mqmgetmodel(result)

kbroman/qtl documentation built on Jan. 13, 2024, 10:14 p.m.