PMC:4564992 / 34222-35185 JSONTXT

{"project":"2_test","denotations":[{"id":"26320892-21181895-2052546","span":{"begin":326,"end":328},"obj":"21181895"}],"text":"Figure S3 shows the type I error of the different EMIM tests, and dashed lines show the expected FWERs if the eight SNPs in the simulated haplotype are (conservatively) considered to be independent. The type I error of the previous version of EMIM (labeled “unknown”), which has been extensively evaluated by Ainsworth et al.,20 acts as a guide to the “correct” type I error rate, allowing for dependency between the SNPs. The type I error when using SHAPEIT2 with fast parameter options is very inflated. This is illustrated further in the Q-Q plots (Figure 4) in which the genomic control inflation factor λ = 1.653. However, the inflation factor can be reduced to 1.052 when using PREMIM’s adjustment procedure. The improvement obtained from adjustment when using the default (slower) parameter options in SHAPEIT2 is not as pronounced: the inflation factor is 1.146 for the unadjusted analysis and reduces to 1.061 when the counts are adjusted (see Figure 4)."}