Fig. 2: Comparison of the performance of different LD approximation strategies. | Nature Communications

Fig. 2: Comparison of the performance of different LD approximation strategies.

From: Accurate and efficient estimation of local heritability using summary statistics and the linkage disequilibrium matrix

Fig. 2

Simulated phenotypes using real genotypic data from UK Biobank, array SNPs on chromosome 22 with MAF > 0.01 (n = 332, 430, p = 9, 220). Labels of the approximation strategies are explained in Table 2. b denotes the bandwidth of the banded component. r denotes the number of factors in the low-rank component. a Approximation accuracy, measured by \(| | \widetilde{{{{{{{{\bf{R}}}}}}}}}| {| }_{F}/| | {{{{{{{\bf{R}}}}}}}}| {| }_{F}\), where \(\widetilde{{{{{{{{\bf{R}}}}}}}}}\) is the approximated LD matrix. Dotted lines are the reference levels: red—85%; blue—95%. b \({h}_{SNP}^{2}\) estimates from 100 simulations. Red reference line represents the true heritability value of 0.25. The upper (lower) whisker extends from the mean to the values 1.96 × SE above (below) the mean. The “LR_only" approximations lead to large bias in h2 estimation, so are omitted from the comparison.

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