Table 2 Parameter choices for the simulation scenarios
From: An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies
Simulation scenario | (μ 1,μ 2) | (σ 1,σ 2) | σ jk | ρ | α (0) | α (1)−α (0) a | |
|---|---|---|---|---|---|---|---|
1 | Distinct differences | (−0.05,0.5) | (0.05, 0.75) | Unif(0.1, 2) | 100 | \(\left [\begin {array}{c} 0.57 \\[-5pt] 0.43 \end {array}\right ]\) | \(\left [\begin {array}{r}0.08 \\[-5pt] -0.08\end {array}\right ] \) |
2 | No confounding | (0.25, 0.25) | (0.5, 0.5) | 0.1 | 100 | \(\left [\begin {array}{c} 0.57 \\[-5pt] 0.43 \end {array}\right ]\) | \(\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]\) |
3 | Opposite effects | (−0.75,0.75) | (0.1, 0.1) | 0.1 | 100 | \(\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]\) | \(\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]\) |
4 | High precision | (0.3, 0.1) | (0.1, 0.1) | 0.1 | 200 | \(\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]\) | \(\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]\) |
5 | Low precision | (0.3, 0.1) | (0.1, 0.1) | 0.1 | 10 | \(\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]\) | \(\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]\) |
6 | Continuous phenotype | (−0.05,0.25) | (0.05, 0.15) | 0.1 | 100 | \(\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]\) | \(\left [\begin {array}{r}0.03 \\[-5pt] -0.03 \end {array}\right ]\) |
7 | Few assoc. sites | (1, 0.95) | (0.05, 0.05) | Unif(0.1, 2) | 100 | \(\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]\) | \(\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]\) |
8 | Many assoc. sites block 1 b | (0.1,0.4) | (0.01, 0.01) | Unif(0.1, 2) | 100 | \(\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]\) | \(\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]\) |
Many assoc. sites block 2 c | (0.2,0.7) | (0.01, 0.01) | Unif(0.1, 2) | 100 | \(\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]\) | \(\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]\) |