Extended Data Fig. 7: Comparison of genomic inflation and power between fastGWA, fastGWA-LOCO, and fastGWA-Ped.
From: A resource-efficient tool for mixed model association analysis of large-scale data
Shown are the results from the analyses of a simulated data set based on the simulation strategy described in part 5 of the Supplementary Note (with \(\sigma _g^2 = 0.4V_p\), \(\sigma _c^2 = 0.1V_p,\,or\,0.2V_p\) for all 1st and 2nd relatives and \(\sigma _c^2 = 0\) for all unrelated individuals). We did not observe any increase in power when applying the LOCO scheme to fastGWA because fastGWA estimates pedigree relatedness by a sparse GRM, to model phenotypic covariance between close relatives due to genetic and/or common environmental effects, and the pedigree relatedness estimated using all autosomes are similar to those using 21 chromosomes under the LOCO scheme. Each boxplot represents the distribution of estimates (that is, median λ, or mean χ2) across 100 simulation replicates. The line inside each box indicates the median value, notches indicate the 95% confidence interval of the median, the central box indicates the interquartile range (IQR), and whiskers indicate data up to 1.5 times the IQR.
