Overview

We will learn how to connect phenotypes and genomics using genomic best linear unbiased prediction (GBLUP).

Use the function load() to load the phenotype object dat_day17.Rda, the OLS fit object fit_day17.Rda, the numerator relationship matrix A2.Rda, the genotype matrix W.Rda, and the results from pedigree-based BLUP day18.Rda we created in class.

load(file.choose())  # dat_day17.Rda
dim(dat)
summary(fit)
dim(A2)
dim(W)

ls()

Statistical model

The statistical model we will fit is given by $\mathbf{y} = \mathbf{X}\mathbf{b} + \mathbf{Z}\mathbf{u} + \mathbf{e},$ where $$\mathbf{y}$$ is the vector of birth weights, $$\mathbf{X}$$ and $$\mathbf{Z}$$ are incident matrices for fixed and random effects, respectively, $$\mathbf{b}$$ is the vector of regression coefficients for fixed effects, $$\mathbf{u}$$ is the vector of regression coefficients for random genetic values, and $$\mathbf{e}$$ is the vector of residuals. Recall that BLUP of $$\mathbf{u}$$ is given by Henderson (1975) (doi: 10.2307/2529430) \begin{align*} BLUP(\mathbf{u}) &= E(\mathbf{u} | \mathbf{y}) \\ &= Cov(\mathbf{u}, \mathbf{y}') Var(\mathbf{y})^{-1} [\mathbf{y} - E(\mathbf{y})] \\ &= \mathbf{G}\sigma^2_{G} \mathbf{Z}'\mathbf{V}^{-1}(\mathbf{y} - \mathbf{X}\hat{\mathbf{b}}), \end{align*} where \begin{align*} \mathbf{V} &= Var(\mathbf{y}) \\ &= \mathbf{Z}\mathbf{G}\sigma^2_G\mathbf{Z}' + \mathbf{I}\sigma^2_e \end{align*}

We predict genomic estimated breeding values (GEBV) or genetic values $$\hat{\mathbf{u}}$$ in the following two steps.

• fit OLS to estimate fixed effects ($$\hat{\mathbf{b}}$$)
• fit BLUP to obtain GEBV ($$\hat{\mathbf{u}}$$) condition on the estimated $$\hat{\mathbf{b}}$$

Later we will discuss how to obtain $$\hat{\mathbf{b}}$$ and $$\hat{\mathbf{u}}$$ simultaneously.

Computing a genomic relationship matrix (G)

We will compute the $$\mathbf{G}$$ matrix defined by VanRaden (2008). The function computeG() accepts two arguments: 1) a genotype matrix and 2) a cutoff point for minor allele frequency (MAF).

computeG <- function(W, maf) {
p <- colMeans(W)/2
maf2 <- pmin(p, 1 - p)
index <- which(maf2 < maf)
W2 <- W[, -index]
p2 <- p[-index]
Wc <- scale(W2, center = TRUE, scale = FALSE)
G <- tcrossprod(Wc)/(2 * sum(p2 * (1 - p2)))
return(G)
}

G <- computeG(W, maf = 0.05)
dim(G)

Exercise 1

Create a boxplot comparing elements of the numerator relationship matrix and geomic relationship matrix. What is the correlation between the pedigree relationships and geomic relationships?

Exercise 2

Repeat Exercise 1 by changing the MAF threshold equal to 0.1. Also, what is the correlation between the two $$\mathbf{G}$$ matrices?

Incidence matrix X

We will now contruct each component one by one. First we will create the incidence matrix $$\mathbf{X}$$. We first subset the variable dat by age of dams and sex of calves, and create a new variable dat2. The model.matrix() function returns the incidence matrix $$X$$.

dat2 <- dat[, c("AgeDam.mon.", "SEX")]
X <- model.matrix(~dat2$AgeDam.mon. + dat2$SEX)
dim(X)
head(X)

Incidence matrix Z

Next we will create the incidence matrix $$\mathbf{Z}$$.

Z <- diag(nrow(G))
dim(Z)
diag(Z)

Incidence matrix I

The third incidence matrix we create is $$\mathbf{I}$$.

I <- diag(nrow(G))
dim(I)
diag(I)

Variance components estimation using the varComp package

The varComp() function in the varComp package fits a liner mixed model and estimates variance components ($$\sigma^2_G$$ and $$\sigma^2_e$$) through a restricted maximum likelihood (REML). The variance-covariance structure of $$\mathbf{u}$$ (argument = varcov) is given by the genomic relationship matrix $$\mathbf{G}$$.

install.packages("varComp")
library(varComp)
?(varComp)

y <- dat$BWT varcomp <- varComp(fixed = y ~ -1 + X, random = ~Z, varcov = G) sigma2G <- varcomp$varComps  # additive genomic variance
sigma2G
sigma2e <- varcomp$sigma2 # residual variance sigma2e Exercise 3 What is the estimate of genomic heritability? Compare the estimate with the one we obtained from the pedigree relationship matrix. Inverse of V Here we compute the inverse of $$V$$ matrix. We will use 1) the multiplication operator %*% and 2) the function solve() to obtain the inverse of matrix. V <- Z %*% G %*% t(Z) * sigma2G + I * sigma2e dim(V) Vinv <- solve(V) dim(Vinv) GBLUP of genetic values Now we compute GEBV ($$\hat{\mathbf{u}}$$). uhatG <- sigma2G * G %*% t(Z) %*% Vinv %*% (matrix(y) - matrix(predict(fit))) uhatG2 <- sigma2G * G %*% t(Z) %*% Vinv %*% (matrix(y) - matrix(X %*% fit$coefficients))  # alternative
table(uhatG == uhatG2)
tail(uhatG)

Let’s plot a histogram of GEBV.

hist(uhatG, col = "lightblue", main = "Histogram", xlab = "Genomic estimated breeding values")

Exercise 4

Create a scatter plot of GEBV vs. observed values. Interpret the result.

Exercise 5

Which individual has the highest GEBV? Which individual has the lowest GEBV? Use the which.max() and which.min() functions.

Exercise 6

Rank animals based on their GEBV. Show the top six animal IDs and their GEBV. Use the order() function.

Exercise 7

Create a scatter plot of EBV vs. GEBV. Compute Spearman’s rank correlation coefficient.

Variance components estimation using the regress package

The regress function in the regress package can also fit a liner mixed model and estimate variance components ($$\sigma^2_G$$ and $$\sigma^2_e$$) through REML.

install.packages("regress")
library(regress)
?(regress)

varcomp2 <- regress(y ~ -1 + X, ~G)
summary(varcomp2)

Exercise 6

What is the estimate of genomic heritability based on the regress() function? Compare the estimate with the one we obtained from the varComp() function.

Save as R object

save(uhatG, h2G, h2G.a, G, file = "day20.Rda")

March 16, 2017