Extended Data Fig. 5: Comparison of false positive rate (FPR) among different association methods.
From: A resource-efficient tool for mixed model association analysis of large-scale data
We used the simulated data as presented in Figs. 1 and 2 to compute the FPR of each association method across different simulation scenarios with different levels of common environmental effects. Each boxplot represents the distribution of FPR 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), whiskers indicate data up to 1.5 times the IQR and outliers are shown as separate dots. In each simulation replicate, the P value of each variant was calculated based on the reported effect estimate and s.e. using a \(\chi _{df = 1}^2\) test.
