Methods | Basis expansions | Priors | Residual covariances |
---|---|---|---|
VBfun | βj = Ψk×mαj, where Ψk×m are the B-spline bases | Diagonal or AR(1) | |
VBnonfun | βj = Ik×kαj, where Ik×k is an identity matrix | Diagonal or AR(1) |
VBfun | VBnonfun | |||
---|---|---|---|---|
Marker | Wald score | Marker | Wald score | Closest simulated QTL |
35 (0.4029) | 320.68 | 35 (0.4029) | 270.29 | (0.4525) 36–37a |
37 (0.4447) | 5037.53 | 37 (0.4447) | 4874.49 | (0.4525) 36–37a |
81 (0.9137) | 183.05 | 81 (0.9137) | 107.43 | (0.8765) 77–78b |
99 (1.0516) | 1114.62 | None | None | (1.0455) 98–99a |
115 (1.2566) | 220.05 | 115 (1.2566) | 171.32 | (1.3302) 118–119c |
138 (1.4852) | 130.74 | 138 (1.4852) | 95.57 | (1.4889) 138–139b |
140 (1.5242) | 143.13 | 140 (1.5242) | 169.91 | (1.4889) 138–139b |
178 (1.9011) | 155.87 | 178 (1.9011) | 164.75 | (1.8864) 174–175a |
222 (2.3108) | 139.91 | 222 (2.3108) | 127.97 | (2.2622) 216–217b |
None | None | 288 (3.048) | 126.70 | (3.0962) 293–294b |
338 (3.7168) | 248.46 | 338 (3.7168) | 171.26 | (3.6979) 336–337a |
None | None | 358 (3.8517) | 65.43 | (3.8639) 358–359b |
415 (4.6311) | 90.95 | 415 (4.6311) | 70.41 | (4.5971) 411–412c |
None | None | 452 (4.9494) | 62.84 | (4.7719) 432–433a |
Descriptions | Trend functions |
---|---|
The intercept with a logistic growth curve | |
Loci 52 and 358 have constant effects over time | β52 = 2 |
β358 = 1 | |
Locus 118 has linear growth effect over time | β118 = 0.1t + 1 |
Loci 174 and 216 are active only at the early stage | |
Loci 98 and 433 are active only at the late stage | |
Locus 78 is active only at the middle stage | |
Locus 35 has the periodic effects over time | β35 = 2 + 2sin(πt / 12) |
k = 10 | k = 10 | k = 100 | k = 100 | |||||
---|---|---|---|---|---|---|---|---|
u = 0.5 | k = 0.8 | u = 0.5 | u = 0.8 | |||||
h2 = 0.2265 | h2 = 0.0922 | h2 = 0.2347 | h2 = 0.1259 | |||||
QLT effects | F | N | F | N | F | N | F | N |
β0 | 0.2194 | 2.0375 | 0.4933 | 14.5590 | 0.0246 | 1.7757 | 0.1166 | 19.4684 |
β35 | 0.0704 | 0.1483 | 0.1138 | 0.5161 | 0.0189 | 0.1267 | 0.0573 | 0.5326 |
β52 | 0.2535 | 0.7231 | 0.0616 | 3.9968 | 0.0247 | 0.2045 | 0.0324 | 3.9995 |
β78 | 0.0921 | 0.1037 | 0.0937 | 0.1542 | 0.0248 | 0.1185 | 0.1442 | 1.2072 |
β98 | 0.1505 | 0.0725 | 0.4961 | 0.5038 | 0.0160 | 0.2116 | 0.4147 | 1.5341 |
β118 | 0.0127 | 0.0239 | 0.1416 | 0.1495 | 0.0063 | 0.0695 | 0.0185 | 0.1778 |
β174 | 0.0513 | 0.7201 | 0.1866 | 0.7229 | 0.0129 | 0.7464 | 0.1099 | 0.7473 |
β216 | 0.0459 | 0.0586 | 0.2224 | 0.0369 | 0.0099 | 0.0606 | 0.0677 | 1.1692 |
β358 | 0.0069 | 0.0493 | 0.0385 | 0.9960 | 0.0022 | 0.0481 | 0.0085 | 0.9988 |
β433 | 0.2278 | 0.0278 | 0.2753 | 2.2965 | 0.0332 | 0.1145 | 0.3022 | 2.3295 |
14.8034 | 14.7677 | 14.9339 | 14.9758 | 14.9081 | 14.9560 | 15.0325 | 15.1299 | |
E[ρ] | 0.5088 | 0.5138 | 0.7796 | 0.7882 | 0.4987 | 0.5036 | 0.7779 | 0.7876 |
n = 200 | n = 200 | n = 500 | n = 500 | |||||
---|---|---|---|---|---|---|---|---|
k = 10 | k = 100 | k = 10 | k = 100 | |||||
QTL | F | N | F | N | F | N | F | N |
35 | 50 | 47 | 50 | 0 | 50 | 50 | 50 | 50 |
52 | 4 | 0 | 49 | 0 | 44 | 0 | 50 | 0 |
78 | 0 | 0 | 50 | 0 | 37 | 3 | 50 | 0 |
98 | 0 | 0 | 45 | 0 | 36 | 0 | 50 | 0 |
118 | 49 | 43 | 50 | 0 | 50 | 50 | 50 | 50 |
174 | 0 | 0 | 11 | 0 | 2 | 0 | 46 | 0 |
216 | 19 | 1 | 49 | 0 | 47 | 38 | 50 | 0 |
358 | 4 | 0 | 50 | 0 | 43 | 0 | 50 | 0 |
433 | 0 | 0 | 43 | 0 | 27 | 0 | 50 | 0 |
Average false positive | 0.04 | 0.04 | 0.32 | 0 | 0.06 | 0.07 | 0.08 | 0 |
n = 200 | n = 200 | n = 500 | n = 500 | |||||
---|---|---|---|---|---|---|---|---|
k = 10 | k = 100 | k = 10 | k = 100 | |||||
QTL | F | N | F | N | F | N | F | N |
Diagonal | 0.08 | 0 | 0.38 | 0 | 0.08 | 0 | 0.40 | 0 |
AR(1) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Marker | Chromosome | Location (cM) | Wald score |
---|---|---|---|
16 (rs13476259) | 1 | 81.40 | 148.6427 |
123 (rs6207781) | 9 | 20.74 | 122.1237 |
140 (rs3654717) | 10 | 55.93 | 110.5854 |