Additive Genomic Relationship Matrix

Description

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

Usage

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

Arguments

X

marker matrix

lambda

numeric scalar, shrinkage parameter

yang

boolean, diagonal elements of A according to Yang et al. (2010)

Details

...

Value

Additive genomic relationship matrix with dimension nrow(X)

Author(s)

Claas Heuer

References

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.

See Also

cgrm, cgrm.D

Examples

1
2
3
4
5
6
7
8
## 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)