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 |
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.
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