# R code for the example with a QTL affecting a specific quantitative trait
            
y<-matrix(c(95.9, 108.0, 96.5, 92.9, 101.0, 94.5, 93.7, 89.8,
            101.2, 103.9, 85.9, 109.4, 105.7, 98.4, 84.1, 103.1,
            117.1, 95.2, 106.4, 104.7, 92.5, 123.9, 97.8, 100.5),nrow=24)

X<-matrix(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
    -1, -1, -1, -1, -1, -1, -1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1), nrow=24)
    
b <- solve(t(X) %*% X) %*% t(X) %*% y

# Using package lm

qtl <- X[,2]

plot(qtl,y)

reg <- lm(y ~ qtl)
summary(reg)

library(multcomp)
m1 <- lm(y ~ 0 + factor(qtl))
summary(m1)

# Contrast for additive effect
K<-matrix(c(-0.5,0,0.5),1)
t<-glht(m1, linfct = K)
summary(t)

# Contrast for dominance effect
K<-matrix(c(-0.5,1,-0.5),1)
t<-glht(m1, linfct = K)
summary(t)