# NOT RUN {
# Use the multitrait dataset
data(multitrait)
# }
# NOT RUN {
multitrait <- calc.genoprob(multitrait)
result <- mqmpermutation(multitrait,pheno.col=7, n.perm=2, batchsize=2)
# }
# NOT RUN {
#Set 50 cofactors
cof <- mqmautocofactors(multitrait,50)
# }
# NOT RUN {
multitrait <- fill.geno(multitrait)
result <- mqmpermutation(multitrait,scanfunction=mqmscan,cofactors=cof,
pheno.col=7, n.perm=2,batchsize=2,verbose=FALSE)
#Create a permutation object
f2perm <- mqmprocesspermutation(result)
#Get Significant LOD thresholds
summary(f2perm)
# }
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