sommer (version 4.3.6)

H.mat: Combined relationship matrix H

Description

Given a matrix A and a matrix G returns a H matrix with the C++ Armadillo library.

Usage

H.mat(A, G, tau = 1, omega = 1, tolparinv=1e-6)

Value

H Matrix with the relationship between the individuals based on pedigree and corrected by molecular information

Arguments

A

Additive relationship matrix based on pedigree.

G

Additive relationship matrix based on marker data.

tau

As described by Martini et al. (2018).

omega

As described by Martini et al. (2018).

tolparinv

Tolerance parameter for matrix inverse used when singularities are encountered in the estimation procedure.

Details

See references

References

Covarrubias-Pazaran G (2016) Genome assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11(6): doi:10.1371/journal.pone.0156744

Martini, J. W., Schrauf, M. F., Garcia-Baccino, C. A., Pimentel, E. C., Munilla, S., Rogberg-Munoz, A., ... & Simianer, H. (2018). The effect of the H-1 scaling factors tau and omega on the structure of H in the single-step procedure. Genetics Selection Evolution, 50(1), 16.

See Also

The core functions of the package mmer

Examples

####=========================================####
####random population of 200 lines with 1000 markers
####=========================================####
M <- matrix(rep(0,200*1000),200,1000)
for (i in 1:200) {
  M[i,] <- sample(c(-1,0,0,1), size=1000, replace=TRUE)
}
rownames(M) <- 1:nrow(M)
v <- sample(1:nrow(M),100)
M2 <- M[v,]

A <- A.mat(M) # assume this is a pedigree-based matrix for the sake of example
G <- A.mat(M2)

H <- H.mat(A,G)
# colfunc <- colorRampPalette(c("steelblue4","springgreen","yellow"))
# hv <- heatmap(H[1:15,1:15], col = colfunc(100),Colv = "Rowv")