Extended Data Fig. 3: Reduced-complexity heritability models.
From: Evaluating and improving heritability models using summary statistics
The seven-parameter BLD-LDAK-Lite is a reduced version of the BLD-LDAK Model, obtained by removing two of the nine continuous annotations and all 57 binary annotations (Supplementary Table 8 explains how we used forward stepwise selection to decide which of the continuous annotations to retain). The nine-parameter BLD-LDAK-Lite+1Fun Model adds to the BLD-LDAK-Lite Model one function indicator and the corresponding 500 base pair buffer, while the eight-parameter BLD-LDAK-Lite+Alpha Model is the same as the BLD-LDAK-Lite Model, except annotations are scaled by [fj(1-fj)]1+α. These plots show that estimates of SNP heritability and confounding bias from the BLD-LDAK-Lite Model, and average estimates of functional enrichments from the BLD-LDAK-Lite+1Fun Model are close to the those from the BLD-LDAK Model, while estimates of α from the BLD-LDAK-Lite+Alpha Model are close to those from the BLD-LDAK + Alpha Model. Numbers indicate how many of the pairs of estimates are inconsistent either nominally or after Bonferroni correction. Numerical values are provided in Supplementary Tables 3–7.
