Function to calculate genomic relationship matrix (GRM)
calcGRM(
genoMat,
methodGRM = "addNOIA",
subpop = NULL,
kernel.h = "tuned",
returnWMat = FALSE,
probaa = NULL,
probAa = NULL
)genomic relationship matrix (GRM)
A \(N \times M\) matrix of marker genotype
Method to calculate genomic relationship matrix (GRM). We offer the following methods; "addNOIA", "domNOIA", "A.mat", "linear", "gaussian", "exponential", "correlation". For NOIA methods, please refer to Vitezica et al. 2017.
Sub-population names corresponding to each individual. By utilizing `subpop` argument, you can consider the difference of allele frequencies between sub-populations when computing the genomic relationship matrix. This argument is only valid when NOIA methods are selected.
The hyper parameter for gaussian or exponential kernel. If kernel.h = "tuned", this hyper parameter is calculated as the median of off-diagonals of distance matrix of genotype data.
If this argument is TRUE, we will return W matrix instead of GRM. Here, W satisfies \(GRM = W W ^ {T}\). W corresponds to H matix in Vitezica et al. 2017.
Probability of being homozygous for the reference allele for each marker. If NULL (default), it will be calculated from genoMat.
Probability of being heterozygous for the reference and alternative alleles for each marker If NULL (default), it will be calculated from genoMat.
Vitezica, Z.G., Legarra, A., Toro, M.A. and Varona, L. (2017) Orthogonal Estimates of Variances for Additive, Dominance, and Epistatic Effects in Populations. Genetics. 206(3): 1297-1307.
Endelman, J.B. and Jannink, J.L. (2012) Shrinkage Estimation of the Realized Relationship Matrix. G3 Genes, Genomes, Genet. 2(11): 1405-1413.