kinship_gcta_limit: Limit of ROM version of the 2011 GCTA kinship (GRM) estimator

In OchoaLab/popkinsuppl: Supplement to popkin package

Limit of ROM version of the 2011 GCTA kinship (GRM) estimator

Description

This function calculates the biased limiting expectation of the GCTA kinship estimator described in Yang et al. (2011), which they refer to as a GRM instead, except the ratio-of-means (ROM) version (the above publication defines the mean-of-ratios (MOR) version instead; see Ochoa and Storey 2021 for the ROM version). The GCTA software history shows that this exact estimator was abandoned in version 0.93.0 (8 Jul 2011) in favor of kinship_std(), which remains in use as of writing (2022). This limit is calculated from the true kinship matrix. It agrees with kinship_std_limit() off-diagonal, but the diagonal bias is slightly different.

Usage

kinship_gcta_limit(kinship)

Arguments

kinship

The true kinship matrix

Value

The biased limit of the GCTA kinship (GRM) estimator

See Also

Standard kinship estimator kinship_std() and the limit of the ROM version kinship_std_limit().

GCTA software, including history/update log. https://yanglab.westlake.edu.cn/software/gcta/#Download

Examples

# create a dummy kinship matrix
kinship <- matrix(
    c(
        0.6, 0.1, 0,
        0.1, 0.6, 0.1,
        0, 0.1, 0.6
        ),
    nrow = 3
)
# this is its biased limit
kinship_gcta_lim <- kinship_gcta_limit(kinship)

OchoaLab/popkinsuppl documentation built on May 17, 2022, 9:50 a.m.