Table 1 Mean numbers of SNPs and prognostic SNPs included in fitted prediction models, recovery rate and means/standard deviations of the log-rank p-value from test sets for the proposed method and methods assuming recessive, dominant, or multiplicative models for all SNPs
From: Prediction of a time-to-event trait using genome wide SNP data
Censoring | ρ | Genetic | Mean number | Mean number of | Recovery | Mean (SD) p-value |
|---|---|---|---|---|---|---|
model | of selected | of selected | rate | of the log-rank | ||
SNPs | prognostic SNPs | test | ||||
30% | 0 | Proposed | 6.72 | 5.05 | 0.75 | <0.0001 (<0.0001) |
Recessive | 8.03 | 4.01 | 0.50 | 0.0052 (0.0018) | ||
Dominant | 6.66 | 3.85 | 0.58 | <0.0001 (<0.0001) | ||
Multiplicative | 7.72 | 4.95 | 0.64 | 0.0004 (0.0003) | ||
0.3 | Proposed | 6.51 | 4.83 | 0.74 | 0.0001 (0.0001) | |
Recessive | 7.73 | 3.83 | 0.50 | 0.0045 (0.0016) | ||
Dominant | 6.58 | 3.66 | 0.56 | 0.0011 (0.0007) | ||
Multiplicative | 7.52 | 4.72 | 0.63 | 0.0006 (0.0004) | ||
15% | 0 | Proposed | 6.65 | 5.18 | 0.78 | <0.0001 (<0.0001) |
Recessive | 8.59 | 4.19 | 0.49 | 0.0028 (0.0011) | ||
Dominant | 6.69 | 3.88 | 0.58 | <0.0001 (<0.0001) | ||
Multiplicative | 7.96 | 4.98 | 0.63 | 0.0005 (0.0005) | ||
0.3 | Proposed | 6.37 | 4.98 | 0.78 | <0.0001 (<0.0001) | |
Recessive | 7.88 | 3.94 | 0.50 | 0.0048 (0.0028) | ||
Dominant | 6.38 | 3.74 | 0.59 | 0.0011 (0.0011) | ||
Multiplicative | 7.55 | 4.89 | 0.65 | 0.0001 (<0.0001) |