cgrm.A: Additive Genomic Relationship Matrix
In cgenpp: Parallel genomic evaluations

Description Usage Arguments Details Value Author(s) References See Also Examples

Based on a marker matrix \mathbf{X} with {-1,0,1} - coding that will be centered column-wise and a shrinkage parameter λ, cgrm.A returns the following additive genomic relationship matrix according to VanRaden (2008):

\mathbf{G} = (1-λ) \frac{\mathbf{X X}^{'}}{∑\limits_{i=1}^n 2 p_i q_i} + \mathbf{I}λ

1	cgrm.A(X, lambda=0, yang=FALSE)

`X`	marker matrix
`lambda`	numeric scalar, shrinkage parameter
`yang`	boolean, diagonal elements of A according to Yang et al. (2010)

...

Additive genomic relationship matrix with dimension nrow(X)

Claas Heuer

VanRaden, P.M. "Efficient Methods to Compute Genomic Predictions". Journal of Dairy Science 91, no. 11 (November 2008): 4414-23. doi:10.3168/jds.2007-0980.

Yang, Jian, Beben Benyamin, Brian P McEvoy, Scott Gordon, Anjali K Henders, Dale R Nyholt, Pamela A Madden, et al. "Common SNPs Explain a Large Proportion of the Heritability for Human Height". Nature Genetics 42, no. 7 (July 2010): 565-69. doi:10.1038/ng.608.

cgrm, cgrm.D

## Not run: 
# generate random data
rand_data(500,5000)

### compute the additive genomic relationship matrix
A <- cgrm.A(M,lambda=0.01)

## End(Not run)