nih-gov/www.niehs.nih.gov/sites/default/files/2024-07/trimmest_tables_508.csv

1	https://www.niehs.nih.gov/research/resources/software/biostatistics/trimmest/index.cfm
2	TRIMMEST Table 1
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4	Carayol's Model	Number of SNPS in haplotype	Risk haplotype frequency	R1 used for generating simulated data	R2 used for generating simulated data	Patten of missingness*	Estimated risk haplotype frequency	Geometric mean of estimated R1 (95% CI)	Geometric mean of estimated R2 (95% CI)	Empirical coverage of nominal 95% confidence interval for R1	Empirical coverage of nomincal 95% confidence interval for R2
5	1	3	0.4	1.5	4	No missing	0.4	1.51 (1.5, 1.52)	4.02 (3.98, 4.07)	0.94	0.944
6					5.3% missing	0.4	1.51 (1.49, 1.52)	4.01 (3.97, 4.06)	0.954	0.944
7						15% missing	0.4	1.51 (1.5, 1.52)	4.03 (3.98, 4.08)	0.94	0.93
8	2	3	0.1	4	11	No missing	0.1	4.03 (3.99, 4.06)	11.14 (10.94, 11.34)	0.946	0.94
9						5.3% missing	0.1	4.03 (4, 4.07)	11.15 (10.93, 11.36)	0.956	0.942
10						15% missing	0.1	4.04 (4, 4.07)	11.15 (10.93, 11.37)	0.94	0.93
11	3	6	0.4	1.5	4	No missing	0.4	1.5 (1.49, 1.51)	4.01 (3.97, 4.06)	0.968	0.954
12						2.7% missing	0.4	1.5 (1.49, 1.51)	4.01 (3.97, 4.06)	0.962	0.958
13						15% missing	0.4	1.5 (1.49, 1.51)	4.02 (3.97, 4.06)	0.97	0.946
14	4	6	0.1	4	11	No missing	0.1	4. (3.96, 4.04)	10.9 (10.72, 11.09)	0.936	0.944
15						2.7% missing	0.1	3.99 (3.96, 4.03)	10.87 (10.69, 11.07)	0.942	0.94
16						15% missing	0.1	4.01 (3.97, 4.05)	10.96 (10.76, 11.16)	0.936	0.948
17	*This column represents the percentage of genotypes missing randomly, which is different from the missingness defined by Carayol et al. (the probability for an individual to have at least one unobserved SNP in a haplotype). Our scenarios of 5.3% and 15% missing genotypes correspond to their 15% and 39% missingness respectively.
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21	TRIMMEST Table 2
22	Pattern of missingness*	Disequilibrium coefficient	Frequence of genotypes with 0, 1, and 2 copies of the risk haplotypes	Geometric mean of estimated R1 (95% CI)	Geometric mean of estimated R2 (95% CI)	Empirical coverage of nominal 95% confidence interval for (R1, R2)
23	No missing	0.1	(0.46, 0.28, 0.26)	1.50(1.49, 1.51)	4.02(3.97, 4.06)	0.952
24	20% missing		(0.46, 0.28, 0.26)	1.51 (1.50, 1.52)	4.03 (3.98, 4.08)	0.959
25	No missing	-0.1	(0.26, 0.68, 0.06)	1.550 (1.450, 1.51)	4.01(3.98, 4.04)	0.948
26	20% missing		(0.26, 0.68, 0.06)	1.51(1.50, 1.52)	4.01(3.98,4.04)	0.946
27	Note: Simulation conditions is Model 1 of Carayol et al. A total of 6 haplotypes comprised of 3 SNPs; risk haplotype frequency=0.4 * Our 20% missing genotypes correspond to Carayol et al's 49% missingness.
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