Figure B.1.1. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of heritability for quantitative traits and variance model 2. The sample size is 1000 and ρ=0.5. The percentage of the causal variants is 0.1. All causal variants are risk variants. The total number of traits is 10. This set of simulations is based on Sgene1.
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Figure B.1.2. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of percentage of protective variants for quantitative traits and variance model 2. The sample size is 1000, the percentage of causal variants is 0.2, the total heritability is 0.03, and ρ=0.5. The total number of traits is 10. This set of simulations is based on Sgene1.
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Figure B.1.3. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of the percentage of causal variants for quantitative traits and variance model 2. The sample size is 1000, ρ =0.5, and the total heritability is 0.03.
All causal variants are risk variants. The total number of traits is 10. This set of simulations is based on Sgene1.
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Figure B.1.4. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of heritability for qualitative traits and variance model 1. The sample size is 1000 and ρ=0.5 . The percentage of the causal variants is 0.1. All causal variants are risk variants. The total number of traits is 10. This set of simulations is based on Sgene1.
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Figure B.1.5. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of percentage of protective variants for qualitative traits and variance model 1. The sample size is 1000, the percentage of causal variants is 0.2, the total heritability is 0.03, and ρ =0.5 . The total number of traits is 10. This set of simulations is based on Sgene1.
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Figure B.1.6. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of the percentage of causal variants for qualitative traits and variance model 1. The sample size is 1000, ρ =0.5, and the total heritability is 0.03.
All causal variants are risk variants. The total number of traits is 10. This set of simulations is based on Sgene1.
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Figure B.1.7. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of heritability for qualitative traits and variance model 2. The sample size is 1000 and . The percentage of the causal variants is 0.1. All causal variants are risk variants. The total number of traits is 10. This set of simulations is based on Sgene1.
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Figure B.1.8. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of percentage of protective variants for qualitative traits and variance model 2. The sample size is 1000, the percentage of causal variants is 0.2, the total heritability is 0.03, and ρ=0.5. The total number of traits is 10. This set of simulations is based on Sgene1.
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Figure B.1.9. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of the percentage of causal variants for qualitative traits and variance model 2. The sample size is 1000, ρ =0.5, and the total heritability is 0.02.
All causal variants are risk variants. The total number of traits is 10. This set of simulations is based on Sgene1.
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Figure B.1.10. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of heritability for quantitative traits under variance model 1. The sample size is 1000 and ρ=0.5. The percentage of the causal variants is 0.1.
All causal variants are risk variants. This set of simulations is based on Sgene2
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Figure B.1.11. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of percentage of protective variants for quantitative traits under variance model 1. The sample size is 1000, the percentage of causal variants is 0.2, the total heritability is 0.03, and ρ =0.5. This set of simulations is based on Sgene2.
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Figure B.1.12. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of the percentage of causal variants for quantitative traits under variance model 1. The sample size is 1000 and ρ=0.5, and the total heritability is 0.03. All causal variants are risk variants. The total number of traits is 10. This set of simulations is based on Sgene2.
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Figure B.1.13. Power comparisons of the four tests (WSRR, AWRR, CCA and Single-TOW) for the power as a function of LP for quantitative traits under variance model 1. LP represents the number of traits positively correlated with risk variants. The sample size is 1000 and the total heritability is 0.015. All causal variants are risk variants. The total number of traits is 10. This set of simulations is based on Sgene2.
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Figure B.2.1. Power comparisons of the five tests (SUM_SCORE, TATES, MHT, MHT-O and MANMHT-OVA) for the power as a function of the effect size (model 1). Sample size is 1000. Total number of traits is 20. The significance level is 5 10× −8. The number of replicates is 500. The number of permutations is 108.
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Figure B.3.1. Power comparisons of the six tests (Single-TOW, MSKAT, AWRR, MANOVA, GAMuT and TOWmuT) for the power as a function of within-factor
correlation for models 1-5 and between-factor correlation for model 6 for 10 quantitative traits with covariates. The sample size is 1000. The percentage of the causal variants is 0.2. All causal variants are risk variants and is for models 1-5. Heritabilities for models 1-6 are 0.05, 0.09, 0.08, 0.03, 0.03, and 0.06, respectively.
ρ=0.5
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Figure B.3.1. Power comparisons of the six tests (Single-TOW, MSKAT, AWRR, MANOVA, GAMuT and TOWmuT) for the power as a function of the percentage of protective variants for 10 quantitative traits with covariates. The sample size is 1000. The percentage of the causal variants is 0.2. The between-factor correlation is 0.3 and the within-factor correlation is 0.7.