# NOT RUN {
data(CviCol)
#Randomly change the order of markers across the genome
cvicol <- CviCol[ ,sample(1:ncol(CviCol), ncol(CviCol), replace=FALSE)]
#Constructing linkage map using gibbs method
out <- netmap(cvicol, cross.typ= "inbred", vis= FALSE, ncores=1); out
#Estimated linkage map
map <- out$map; map
#Plot the associated three-dimensional map
plot(out)
#Visualize other three-dimensional maps
plot(out$allres)
#Build a linkage map for 5th three-dimensional map
bm <- buildMap(out, opt.index=5); bm
####################
#Constructing linkage map using approx method
out2 <- netmap(cvicol, method="approx", cross.typ= "inbred", vis= FALSE, ncores=1); out2
#Estimated linkage map
map2 <- out2$map; map2
#Plot the associated 3-dimensional map
plot(out2)
#Visualize other three-dimensional maps
plot(out2$allres)
#Build a linkage map for 5th three-dimensional map
bm2 <- buildMap(out2, opt.index=5); bm2
#Constructing linkage map using npn method
out3 <- netmap(cvicol, method="npn", cross.typ= "inbred", vis= FALSE, ncores=1); out2
#Estimated linkage map
map3 <- out3$map; map3
#Plot the associated 3-dimensional map
plot(out3)
# }
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