11.4 Running lm_markers examples and sample output

lm_markers can be run with all three parameter files in the `Lodscores/' subdirectory. As usual, the syntax for running the program is:

./lm_markers <parameter file>

This section describes the output obtained my using the parameter file `ped73_qu.par'. Note that this file contains an option for peeling by component, see commenting at the end of the parameter file for implementation. The peeling by component option allows for LOD scores to be computed for each component separately, as well as jointly over all components. To run the example, type:

./lm_markers ped73_qu.par

The interesting part of the output is the LodScore estimates. For each test position, we have the LOD score and the standard deviation.

LodScore estimates by Rao-Blackwellized computation: Trait pos # position (Haldane cM) or marker male female LodScore StdErr 1 -115.129 -115.129 0.0312 0.0006 2 -80.472 -80.472 0.0532 0.0012 3 -45.815 -45.815 0.0561 0.0031 4 -17.834 -17.834 -0.0989 0.0078 5 -5.268 -5.268 -0.3636 0.0160 marker-1 0.000 0.000 -0.5626 0.0248 6 3.000 3.000 -0.5639 0.0248 7 7.000 7.000 -0.6048 0.0280 marker-2 10.000 10.000 -0.6660 0.0316 8 13.000 13.000 -0.6474 0.0208 9 17.000 17.000 -0.6788 0.0133 marker-3 20.000 20.000 -0.7628 0.0147 10 23.000 23.000 -0.4993 0.0183 11 27.000 27.000 -0.2416 0.0292 marker-4 30.000 30.000 -0.0863 0.0407 12 33.000 33.000 0.5250 0.0352 13 37.000 37.000 0.9361 0.0275 marker-5 40.000 40.000 1.1317 0.0182 14 43.000 43.000 0.9977 0.0165 15 47.000 47.000 0.7870 0.0153 marker-6 50.000 50.000 0.5955 0.0153 16 53.000 53.000 0.4909 0.0152 17 57.000 57.000 0.2737 0.0151 marker-7 60.000 60.000 0.0359 0.0181 18 63.000 63.000 -0.2081 0.0103 19 67.000 67.000 -0.6324 0.0066 marker-8 70.000 70.000 -1.0908 0.0080 20 73.000 73.000 -0.6078 0.0125 21 77.000 77.000 -0.3453 0.0109 marker-9 80.000 80.000 -0.2890 0.0083 22 83.000 83.000 -0.0640 0.0064 23 87.000 87.000 0.1769 0.0068 marker-10 90.000 90.000 0.3237 0.0107 24 95.268 95.268 0.4945 0.0070 25 107.834 107.834 0.5835 0.0037 26 135.815 135.815 0.3911 0.0014 27 170.472 170.472 0.1810 0.0004 28 205.129 205.129 0.0812 0.0001

For more information regarding the MCMC parameters and diagnostic output, See MCMC parameters and options.