qtl: mqmautocofactors – R documentation

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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)

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 broman@wisc.edu

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)

qtl

Tools for Analyzing QTL Experiments

v1.48-1

GPL-3

Authors

Karl W Broman <broman@wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, Brian Yandell, and R Core Team

Initial release

2021-03-24