Fig. 1: Estimate of ρ2 (y-axis) for the maximum likelihood estimator (Gerard 2021) (MLE), our new moment-based estimator (Eq. (10)) (MoM), and the naive squared sample correlation coefficient between posterior mean genotypes (Eq. (13)) (Naive).
From: Scalable bias-corrected linkage disequilibrium estimation under genotype uncertainty
The x-axis indexes the sample size, the row-facets index the ploidy, and the column-facets index the true ρ2, which is also presented by the horizontal dashed red line. These simulations were performed using a read-depth of 10, and major allele frequencies of 0.5 at each locus. The naive estimator presents a strong attenuation bias toward 0, particularly for higher ploidy regimes.
