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Table 3 Summary of LOD scores for the three penetrance models

From: MLEP: an R package for exploring the maximum likelihood estimates of penetrance parameters

Disease allele frequency Model Recombination fraction(θ)
True value Assumed value 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45
0.0001   True 4.071 3.831 3.535 3.201 2.835 2.438 2.011 1.553 1.066 0.549
0.0001 MLE 3.992 3.797 3.520 3.198 2.838 2.444 2.017 1.559 1.069 0.550
  Dominant -0.158 3.296 3.394 3.240 2.965 2.609 2.189 1.714 1.189 0.617
  True 4.065 3.826 3.530 3.196 2.830 2.434 2.007 1.550 1.063 0.547
0.001 MLE 4.003 3.805 3.527 3.204 2.843 2.448 2.021 1.561 1.071 0.550
  Dominant -0.188 3.265 3.364 3.211 2.939 2.586 2.170 1.698 1.176 0.609
  True 4.022 3.784 3.489 3.157 2.792 2.398 1.974 1.521 1.040 0.532
0.01 MLE 3.984 3.780 3.500 3.175 2.815 2.421 1.995 1.538 1.051 0.538
  Dominant -0.234 3.217 3.320 3.171 2.902 2.552 2.138 1.670 1.155 0.598
  True 3.702 3.474 3.191 2.872 2.524 2.150 1.750 1.328 0.887 0.437
0.1 MLE 3.665 3.429 3.143 2.823 2.476 2.103 1.708 1.292 0.860 0.422
  Dominant -0.425 3.040 3.146 3.002 2.738 2.397 1.997 1.549 1.059 0.534
  True 3.257 3.049 2.787 2.492 2.171 1.827 1.464 1.087 0.704 0.331
0.25 MLE 1.524 1.407 1.270 1.121 0.964 0.800 0.634 0.467 0.303 0.146
  Dominant -0.743 2.748 2.862 2.727 2.478 2.158 1.783 1.362 0.906 0.437
  True 2.549 2.384 2.165 1.917 1.646 1.359 1.061 0.760 0.469 0.205
0.5 MLE -0.009 0.204 0.292 0.321 0.315 0.284 0.238 0.182 0.121 0.059
  Dominant -1.339 2.208 2.349 2.250 2.044 1.765 1.434 1.067 0.682 0.311
0.001   True 4.086 3.846 3.548 3.213 2.846 2.447 2.019 1.560 1.070 0.551
0.0001 MLE 4.008 3.812 3.534 3.210 2.849 2.453 2.025 1.565 1.073 0.552
  Dominant -0.140 3.312 3.409 3.253 2.977 2.619 2.198 1.721 1.193 0.619
  True 4.081 3.841 3.543 3.208 2.841 2.443 2.014 1.556 1.067 0.549
0.001 MLE 4.018 3.820 3.541 3.216 2.854 2.458 2.028 1.567 1.075 0.553
  Dominant -0.170 3.281 3.379 3.225 2.951 2.597 2.179 1.705 1.180 0.611
  True 4.038 3.799 3.502 3.169 2.803 2.407 1.981 1.527 1.044 0.534
0.01 MLE 4.000 3.795 3.513 3.187 2.825 2.429 2.002 1.543 1.055 0.540
  Dominant -0.216 3.234 3.335 3.185 2.915 2.563 2.147 1.677 1.160 0.601
  True 3.717 3.489 3.204 2.884 2.535 2.159 1.757 1.334 0.891 0.439
0.1 MLE 3.602 3.338 3.040 2.717 2.372 2.006 1.621 1.221 0.809 0.394
  Dominant -0.407 3.056 3.161 3.016 2.751 2.407 2.006 1.556 1.064 0.536
  True 3.272 3.063 2.800 2.503 2.181 1.836 1.471 1.093 0.708 0.332
0.25 MLE 1.847 1.667 1.479 1.286 1.090 0.893 0.698 0.508 0.325 0.154
  Dominant -0.725 2.765 2.877 2.741 2.490 2.168 1.792 1.369 0.911 0.439
  True 2.563 2.397 2.177 1.927 1.655 1.366 1.067 0.765 0.471 0.207
0.5 MLE 0.048 0.234 0.310 0.332 0.321 0.288 0.240 0.183 0.121 0.060
  Dominant -1.321 2.225 2.364 2.264 2.056 1.776 1.443 1.073 0.686 0.312
0.01   True 3.808 3.619 3.348 3.038 2.694 2.317 1.909 1.472 1.008 0.517
0.0001 MLE 3.647 3.461 3.206 2.913 2.588 2.231 1.841 1.421 0.973 0.499
  Dominant -0.374 3.002 3.150 3.037 2.794 2.466 2.072 1.621 1.122 0.580
  True 3.863 3.639 3.355 3.038 2.691 2.313 1.905 1.469 1.005 0.515
0.001 MLE 3.730 3.532 3.267 2.964 2.628 2.262 1.864 1.437 0.983 0.503
  Dominant -0.345 3.011 3.136 3.013 2.770 2.444 2.053 1.605 1.109 0.572
  True 3.881 3.637 3.344 3.018 2.664 2.284 1.876 1.442 0.983 0.501
0.01 MLE 3.836 3.623 3.344 3.026 2.677 2.299 1.891 1.455 0.992 0.505
  Dominant -0.329 3.019 3.133 2.998 2.746 2.417 2.025 1.579 1.089 0.562
  True 3.629 3.389 3.101 2.782 2.436 2.067 1.677 1.268 0.844 0.415
0.1 MLE 3.514 3.243 2.944 2.622 2.281 1.922 1.548 1.162 0.767 0.374
  Dominant -0.455 2.907 3.021 2.884 2.628 2.297 1.909 1.478 1.008 0.508
  True 3.224 3.002 2.734 2.437 2.115 1.775 1.418 1.050 0.679 0.319
0.25 MLE 2.100 1.888 1.668 1.445 1.219 0.993 0.772 0.557 0.354 0.166
  Dominant -0.737 2.651 2.774 2.647 2.405 2.093 1.728 1.320 0.879 0.426
  True 2.563 2.384 2.158 1.905 1.632 1.345 1.049 0.752 0.465 0.205
0.5 MLE -0.105 0.150 0.249 0.286 0.286 0.262 0.221 0.170 0.114 0.056
  Dominant -1.289 2.160 2.311 2.219 2.018 1.746 1.422 1.062 0.684 0.315
0.1   True 2.571 3.140 2.984 2.742 2.445 2.105 1.730 1.326 0.900 0.457
0.0001 MLE 2.645 2.809 2.691 2.494 2.245 1.955 1.632 1.276 0.886 0.460
  Dominant -3.354 2.123 2.564 2.607 2.467 2.211 1.869 1.462 1.005 0.513
  True 2.965 3.191 3.011 2.753 2.447 2.103 1.727 1.323 0.897 0.455
0.001 MLE 2.986 3.054 2.898 2.663 2.377 2.051 1.692 1.304 0.891 0.456
  Dominant -2.980 2.115 2.538 2.580 2.442 2.189 1.850 1.446 0.991 0.504
  True 3.319 3.265 3.044 2.763 2.441 2.086 1.705 1.300 0.877 0.442
0.01 MLE 3.223 3.185 2.991 2.731 2.423 2.077 1.701 1.299 0.876 0.441
  Dominant -2.599 2.149 2.524 2.555 2.415 2.161 1.823 1.420 0.971 0.495
  True 3.388 3.185 2.916 2.609 2.274 1.915 1.538 1.149 0.754 0.366
0.1 MLE 3.350 3.133 2.859 2.551 2.218 1.863 1.492 1.111 0.727 0.351
  Dominant -2.344 2.159 2.479 2.473 2.314 2.051 1.713 1.320 0.894 0.446
  True 3.111 2.897 2.627 2.327 2.003 1.662 1.311 0.956 0.608 0.283
0.25 MLE 2.471 2.224 1.967 1.702 1.434 1.165 0.900 0.644 0.403 0.186
  Dominant -2.443 1.991 2.296 2.283 2.120 1.861 1.536 1.169 0.774 0.372
  True 2.561 2.370 2.128 1.859 1.573 1.276 0.978 0.688 0.419 0.184
0.5 MLE 0.240 0.324 0.351 0.344 0.315 0.271 0.217 0.160 0.102 0.048
  Dominant -2.804 1.584 1.892 1.894 1.751 1.522 1.244 0.929 0.596 0.275
0.2   True 1.245 2.462 2.452 2.312 2.096 1.827 1.517 1.174 0.804 0.412
0.0001 MLE 1.471 2.049 2.086 2.006 1.852 1.641 1.383 1.086 0.754 0.392
  Dominant -5.718 1.358 1.978 2.131 2.078 1.898 1.628 1.290 0.898 0.465
  True 1.891 2.542 2.488 2.325 2.099 1.826 1.514 1.171 0.801 0.410
0.001 MLE 2.027 2.354 2.310 2.174 1.976 1.730 1.444 1.122 0.772 0.397
  Dominant -5.102 1.341 1.948 2.100 2.048 1.869 1.602 1.268 0.883 0.458
  True 2.484 2.669 2.544 2.343 2.094 1.808 1.491 1.147 0.781 0.397
0.01 MLE 2.435 2.557 2.448 2.263 2.030 1.757 1.451 1.116 0.759 0.385
  Dominant -4.507 1.360 1.924 2.059 1.997 1.816 1.552 1.227 0.851 0.436
  True 2.763 2.662 2.461 2.218 1.944 1.647 1.332 1.002 0.663 0.323
0.1 MLE 2.684 2.539 2.326 2.081 1.813 1.526 1.226 0.916 0.602 0.291
  Dominant -4.074 1.352 1.847 1.951 1.876 1.694 1.435 1.117 0.756 0.379
  True 2.570 2.425 2.215 1.972 1.705 1.423 1.128 0.828 0.529 0.246
0.25 MLE 1.948 1.755 1.551 1.341 1.128 0.916 0.707 0.506 0.317 0.146
  Dominant -4.071 1.211 1.691 1.789 1.717 1.540 1.290 0.986 0.657 0.320
  True 2.101 1.964 1.775 1.560 1.328 1.085 0.837 0.591 0.360 0.159
0.5 MLE 0.625 0.595 0.545 0.484 0.416 0.343 0.269 0.195 0.125 0.060
  Dominant -4.299 0.868 1.353 1.466 1.413 1.260 1.039 0.781 0.509 0.239