mqmsetcofactors: Set cofactors at fixed intervals, to be used with MQM

In qtl: Tools for Analyzing QTL Experiments

Set cofactors at fixed intervals, to be used with MQM

Description

Set cofactors, at fixed marker intervals. Together with mqmscan cofactors are selected through backward elimination.

Usage

mqmsetcofactors(cross, each = NULL, cofactors=NULL, sexfactors=NULL, verbose=FALSE)

Arguments

cross	An object of class cross. See read.cross for details.
each	Every 'each' marker will be used as a cofactor, when each is used the cofactors and sexfactors parameter is ignored
cofactors	List of cofactors to be analysed in the QTL model. To set cofactors use mqmautocofactors or mqmsetcofactors; when each is set, this parameter is ignored
sexfactors	list of markers which should be treated as dominant cofactors (sexfactors), when each is set, this parameter is ignored
verbose	If TRUE, print tracing information.

Value

An list of cofactors to be passed into 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)
  # Automatic cofactors every third marker
    cofactors <- mqmsetcofactors(hyperfilled,3)
    result <- mqmscan(hyperfilled,cofactors)	# Backward model selection
    mqmgetmodel(result)
  #Manual cofactors at markers 3,6,9,12,40 and 60
  cofactors <- mqmsetcofactors(hyperfilled,cofactors=c(3,6,9,12,40,60))
    result <- mqmscan(hyperfilled,cofactors)	# Backward model selection
    mqmgetmodel(result)

qtl documentation built on Sept. 11, 2024, 5:43 p.m.