Table 1.
Definitions for the true simulated disease/subtype models
| True scenario | Population frequency of A allele |
|||
| U | d | d* | ||
| null | q<LOWER>U</LOWER> | q<LOWER>U</LOWER> | q<LOWER>U</LOWER> | |
| basic | q<LOWER>U</LOWER> | q<LOWER>U</LOWER> + Δ | q<LOWER>U</LOWER> + Δ | |
| subset | q<LOWER>U</LOWER> | q<LOWER>U</LOWER> | q<LOWER>U</LOWER> + Δ | |
| inv-subset | q<LOWER>U</LOWER> | q<LOWER>U</LOWER> + Δ | q<LOWER>U</LOWER> | |
| modifier | q<LOWER>U</LOWER> | q<LOWER>U</LOWER> − Δ (1 − s) | q<LOWER>U</LOWER> + s Δ | |
| gradient | q<LOWER>U</LOWER> | q<LOWER>U</LOWER> + Δ | q<LOWER>U</LOWER> + 2 Δ | |
For each of the three groups (U, d and d*), the allele frequency is parameterized in terms of qU (baseline frequency), Δ (effect of the variant), and s (subtype frequency).