AGHmatrix (version 2.0.0)

Hmatrix: Construction of Combined Relationship Matrix H

Description

Given a matrix A and a matrix G returns a H matrix.

Usage

Hmatrix(
  A = NULL,
  G = NULL,
  markers = NULL,
  c = 0,
  method = "Martini",
  tau = 1,
  omega = 1,
  missingValue = -9,
  maf = 0,
  ploidy = 2,
  roundVar = 3
)

Arguments

A

A matrix from function Amatrix

G

G matrix from function Gmatrix

markers

matrix marker which generated the Gmatrix

c

constant value of H computation, default: c=0

method

"Martini" or "Munoz", default="Martini"

tau

to be used for Martini's method, default=1.

omega

to be used of Martini's method, default=1.

missingValue

missing value in data, default=-9.

maf

max of missing data accepted to each markerm default=0.05.

ploidy

data ploidy (an even number between 2 and 20), default=2.

roundVar

Munoz's method, how many digits to consider the relationship be of same class, default=2.

Value

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

References

Munoz, P. R., Resende, M. F. R., Gezan, S. A., Resende, M. D. V., de los Campos, G., Kirst, M., Huber, D., Peter, G. F. (2014). Unraveling additive from nonadditive effects using genomic relationship matrices. Genetics, 198.4: 1759-1768.

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.

Examples

# NOT RUN {
data(ped.sol)
data(snp.sol)
#Computing the numerator relationship matrix 10% of double-reduction
Amat <- Amatrix(ped.sol, ploidy=4, w = 0.1)
#Computing the additive relationship matrix based on VanRaden (modified)
Gmat <- Gmatrix(snp.sol, ploidy=4, missingValue=-9,
                maf=0.05, method="VanRaden")
#Computing H matrix (Martini)
Hmat_Martini <- Hmatrix(A=Amat, G=Gmat, method="Martini", 
                     ploidy=4, missingValue=-9, maf=0.05)
#Computing H matrix (Munoz)
Hmat_Munoz <- Hmatrix(A=Amat, G=Gmat, markers = snp.sol, 
                      ploidy=4, method="Munoz",
                      roundVar=2,
                      missingValue=-9, maf=0.05)
# }
# NOT RUN {
# }