I need an urgent help from the researchgate community. Can anybody help me to write codes for BLUP model in R (any BLUP package) for the attached data? First column of the .csv file indicate genotypes I used in my project and subsequent columns indicate traits I have measured. I will be grateful if anybody help me in this regard.
Thanks a lot.
Estimating Heritability and Trait BLUPs
hydro=read.csv("hydro.csv", header=T)
## Attach dataset
attach(hydro)
# Rename variables for ease of use
SL= as.numeric(SL)
Gen = as.factor(Gen)
trt = as.factor(trt)
REP = as.factor(rep)
## Examine distribution of brix data
hist(SL, col="gold")
boxplot(SL~trt, xlab="trt", ylab="Degrees SL", main="Degrees SL by trt", col="pink")
## Calculate variance components
# requires lme4 package
library(lme4)
# Linear Model with random effects for variance components
SLvarcomp = lmer(SL~ (1|Gen) + (1|trt) + (1|Gen:trt))
# Extract variance components
summary(SLvarcomp)
## BLUPS
# fit the model
SLmodel = lmer(SL ~ (1|Gen) + (1|trt) + (1|Gen:trt))
# estimate BLUPS
SLblup = ranef(SLmodel)
# look at output structure
str(SLblup)
# extract blup for line
SLGenblup = SLblup$Gen
# see the structure of the blup for each line
str(SLGenblup)
# save the SLGenblup output to a separate .csv file
write.csv(SLGenblup, file="SLGenLUPS.csv")
## Creating plots with the BLUPs
# Create a numeric vector with the BLUP for each line
GenBLUP = SLGenblup[,1]
# Create a histogram with the BLUP for each line
hist(GenBLUP, col="brown")
## Compare BLUP to line averages on a scatterplot
lmean = tapply(SL, Gen, na.rm=T, mean)
plot(GenBLUP, lmean, col="blue")
plot(SLmodel)
boxplot(SL~Gen)
Thank you Dr. Shalim Uddin for your share. I will try the codes, if there is a problem, I will communicate with you. Thanks again. Regards
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