Decompose the scaled genotype matrix. — take.ld.svd • zqtl

Decompose the scaled genotype matrix.

take.ld.svd(X, options, eigen.tol, eigen.reg, do.stdize)

Arguments

X: n x p matrix
options: a list of options
eigen.tol: Error tolerance in Eigen decomposition (default: 0.01)
eigen.reg: Regularization of Eigen decomposition (default: 0.0)
do.stdize: Standardize (default: TRUE)

Details

Decompose \(n^{-1/2}X = U D V^{\top}\) such that the LD matrix can become $$R = V D^{2} V^{\top}$$ for subsequent analysis.