mqmfind.marker {qtl}R Documentation

Fetch significant markers after permutation analysis

Description

Fetch significant makers after permutation analysis. These markers can be used as cofactors for model selection in a forward stepwise approach.

Usage

mqmfind.marker(cross, mqmscan = NULL, perm = NULL, alpha = 0.05, verbose=FALSE)

Arguments

cross An object of class cross. See read.cross for details.
mqmscan Results from either scanone or mqmscan
perm a scanoneperm object
alpha Threshold value, everything with significance < alpha is reported
verbose Display more output on verbose=TRUE

Value

returns a matrix with at each row a significant marker (determined from the scanoneperm object) and with columns: markername, chr and pos (cM)

Author(s)

Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman kbroman@biostat.wisc.edu

See Also

Examples

data(multitrait)				#Use the multitrait dataset
cof <- mqmsetcofactors(multitrait,3)		#Set cofactors at each 3th marker
multitrait <- fill.geno(multitrait)
multitrait <- transformPheno(multitrait, 7)     #log transform the 7th phenotype
## Not run: result <- mqmpermutation(multitrait,scanfunction=mqmscan,cofactors=cof,pheno.col=7,n.perm=50,batchsize=10)	# Bootstrap 50 runs in batches of 10

f2perm <- mqmprocesspermutation(result)		        #Create a permutation object
summary(f2perm)				        #What LOD score is considered significant ?
marker <- mqmfind.marker(multitrait,result[[1]],f2perm)		#Find markers with a significant QTL effect (First run is original phenotype data)
marker						#Print it to the screen

[Package qtl version 1.21-2 Index]