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 | Â | 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 | Â | 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 | Â | 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 | Â | 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 | Â | 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 |