cpgen (version 0.1)

cgrm.D: Dominance Genomic Relationship Matrix

Description

Based on a marker matrix $\mathbf{X}$ with {-1,0,1} - out of which a column-wise centered dominance coefficient matrix will be constructed and a shrinkage parameter $\lambda$, cgrm.D returns the following dominance genomic relationship matrix according to Su et al. (2012): $$\mathbf{G}=(1-\lambda )\frac{{\mathbf{X}\mathbf{X}}^{{}^{\prime }}}{\sum _{i=1}^{n}2p_i{q}_i(1-2p_i{q}_i)}+\mathbf{I}\lambda$$

The additive marker coefficients will be used to compute dominance coefficients as: 1-abs(X)

Usage

cgrm.D(X, lambda=0)

Arguments

X

marker matrix

lambda

numeric scalar, shrinkage parameter

Value

• Dominance relationship matrix with dimension nrow(X)

Details

...

References

Su G, Christensen OF, Ostersen T, Henryon M, Lund MS (2012) "Estimating Additive and Non-Additive Genetic Variances and Predicting Genetic Merits Using Genome-Wide Dense Single Nucleotide Polymorphism Markers". PLoS ONE 7(9): e45293. doi:10.1371/journal.pone.0045293

See Also

cgrm, cgrm.A.

Examples

# generate random data
rand_data(500,5000)

D <- cgrm.D(M,lambda=0.01)