mqmsetcofactors {qtl}R Documentation

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 kbroman@biostat.wisc.edu

See Also

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)

[Package qtl version 1.21-2 Index]