Table 3.
Probabilities describing the relationship between flashfm ranks of causal variants when the trait correlation is mis-specified.
| Trait 1 (E+G) | ||||
|---|---|---|---|---|
| Pr(matched ranks) | Pr(matched or improved ranks) | |||
| Trait correlation shift | rs1980422/E | rs3087243/G | rs1980422/E | rs3087243/G |
| −0.2 | 0.870 | 0.923 | 0.960 | 0.950 |
| −0.1 | 0.903 | 0.950 | 0.970 | 0.967 |
| 0.1 | 0.897 | 0.950 | 0.933 | 0.983 |
| 0.2 | 0.793 | 0.900 | 0.857 | 0.947 |
| Trait 2 (E+H) | ||||
|---|---|---|---|---|
| Pr(ranks match) | Pr(matched or improved ranks) | |||
| Trait correlation shift | rs1980422/E | rs231775/H | rs1980422/E | rs231775/H |
| −0.2 | 0.850 | 0.913 | 0.940 | 0.977 |
| −0.1 | 0.893 | 0.937 | 0.953 | 0.987 |
| 0.1 | 0.870 | 0.960 | 0.920 | 0.973 |
| 0.2 | 0.760 | 0.897 | 0.837 | 0.927 |
Two traits were simulated to have causal variants E+G and E+H and trait correlation 0.4; sample size is N = 3000. Comparisons are made between flashfm results using the estimated trait correlation as input and flashfm results with this trait correlation estimate shifted upwards/downwards by 0.1 or 0.2. The region has 1231 SNPS and was simulated to mimic the LD structure of the CTLA4 region, 2q-204446258-204816382 (GRCh37/hg19). Results are based on 300 replications.