Compute Kinship-Adjusted rV^2 LD Matrix

Computes the kinship-adjusted squared correlation (rV^2) for a pre-whitened genotype matrix \(X = V^{-1/2} \tilde{G}\). The whitening step must be performed first via prepare_geno.

Mathematically identical to compute_r2 applied to \(X\) because the whitening already removes kinship structure. The C++ kernel is the same - the distinction is purely in the preparation step.

Usage

compute_rV2(X, digits = -1L, n_threads = 1L)

Arguments

X

NumericMatrix (n x p). Pre-whitened, mean-centred genotype matrix.

digits

Integer. Rounding. -1 = none.

n_threads

Integer. OpenMP threads.

Value

Symmetric p x p NumericMatrix, diagonal 0.

References

Kim S-A et al. (2018) GENETICS 209(3):855-868.

See also

compute_r2, prepare_geno