makeG: Make genomic relationship matrix using Van Raden (2008)

In digiYozhik/msc_thesis: Functions to support master thesis

Description

Make genomic relationship matrix using Van Raden (2008)

Usage

makeG(x, bAlleleFrequency = NULL)

Arguments

x	matrix of genotypes in bi-allelic format (e.g. AA, AC, CC). Missing data is entered as NA.
bAlleleFrequency	vector of B allele frequencies for the markers. Default is NULL which uses the column means of the vector x in the calculation of the G matrix.

Details

The function first calculates the Z matrix using makeZ, then scales the Z matrix using bAlleleFrequency to obtain the G matrix as defined by Van Raden (2008).

Value

realization of the G matrix in R matrix format

References

Van Raden, P.M. (2008). Efficient methods to compute genomic predictions. Journal of Dairy Science, 91(11): 4412-4423.

See Also

makeZ

Examples

data(M)
head(makeG(M))

digiYozhik/msc_thesis documentation built on May 14, 2019, 5:16 p.m.