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8.6 Sample lm_bayes output

Run the example by typing:

 
lm_bayes par15_bayes

The results from lm_bayes are the LOD scores toward the end of the output. Two methods of computing the LOD scores are available: (1) count realizations of locations sampled to estimate the posterior probability (crude) and (2) Rao-Blackwellized estimator (R-B). The latter is the preferred method.

 
LodScore estimates:
 
Trait pos #     position (Haldane cM)     pseudo     freq        LodScore
  or marker        male     female         prior  visited     crude       R-B
 
          0    unlinked   unlinked      0.072240       11        NA        NA
          1    -115.129   -115.129      0.073157       24    0.3333   -0.0170
          2     -60.199    -60.199      0.073318       11   -0.0064   -0.0398
          3     -34.657    -34.657      0.069086       12    0.0572   -0.0281
          4     -17.834    -17.834      0.057102        3   -0.4621    0.0479
          5      -5.268     -5.268      0.038580        4   -0.1669    0.2009
   marker-1       0.000      0.000            NA       NA        NA        NA
          6       5.108      5.108      0.034398       16    0.4850    0.2780
          7      12.771     12.771      0.036335       18    0.5123    0.2974
          8      20.433     20.433      0.031742       15    0.4918    0.3532
   marker-2      25.541     25.541            NA       NA        NA        NA
          9      30.650     30.650      0.026108        5    0.0996    0.3707
         10      38.312     38.312      0.024442        3   -0.0936    0.3374
         11      45.974     45.974      0.021466        6    0.2638    0.3163
   marker-3      51.083     51.083            NA       NA        NA        NA
         12      56.191     56.191      0.020620        1   -0.4969    0.2723
         13      63.853     63.853      0.021574        1   -0.5165    0.2687
         14      71.516     71.516      0.020624        6    0.2812    0.3134
   marker-4      76.624     76.624            NA       NA        NA        NA
         15      81.732     81.732      0.022869        0        NA    0.3285
         16      89.394     89.394      0.027993        3   -0.1525    0.3172
         17      97.057     97.057      0.030376        4   -0.0631    0.3599
   marker-5     102.165    102.165            NA       NA        NA        NA
         18     107.433    107.433      0.036779        6    0.0299    0.3137
         19     119.999    119.999      0.052239       24    0.4796    0.1360
         20     136.822    136.822      0.064913        1   -0.9949    0.0336
         21     162.364    162.364      0.071376       12    0.0430   -0.0040
         22     217.294    217.294      0.072663       16    0.1602   -0.0054


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