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8.7 Comparison of LOD scores methods

In the examples directory are also included seven examples of MCMC LOD score estimation using data simulated on a single 52-member pedigree. The three programs lm_lods, lm_markers, lm_bayes are run. There are three types of trait data: genotypic, phenotypic (discrete) and quantitative. Details of the data simulation and of the results are given in ped52_lodscores.

To run these examples:

make lm_quant.out
runs lm_markers compiled with QUANT=1 to analze a quantitative trait

make lm_mrks_g.out
runs lm_markers for a genotypic trait

make lm_mrks_p.out
runs lm_markers for a phenotypic trait

make lm_lods_g.out
runs lm_lods for the genotypic trait

make lm_lods_p.out
runs lm_lods for the phenotypic trait

make lm_bayes_g.out
runs lm_bayes for the genotypic trait

make lm_bayes_p.out
runs lm_bayes for the phenotypic trait
You may also:

make lm_quant.test
etc. Use the suffix .test instead of .out with the preceding seven makes to run the same examples using default seeds
make ped52.test
runs all seven examples with default seeds
make ped52.diff
diff's your outputs with provided output files from the seven examples and puts the results in `test.diff'



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