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
make
s 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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