10.2 Sample lm_ibdtests parameter file

The example parameter file for lm_ibdtests, `ped73_ibdt_IBD.par', may be found in the `TraitTests' subdirectory of `MORGAN_Examples'. Several lines in the example parameter file have been explained in previous sections of the tutorial, only the sections requiring additional explanation are shown below.

sample by scan set L-sampler probability 0.5 set burn-in iterations 1000 check progress MC iterations 1000 compute ibd statistics set ibd measures Spairs Srobdom set ibd tests norm permu set ibd permutations 999 compute scores every 100 iterations

The statement `sample by scan' indicates that all loci or all meioses are updated successively in an order determined by random permutation. The alternative `sample by step' updates only one locus (L-sampler) or one meiosis (M-sampler) in each iteration. The `set L-sampler probability' statement specifies that the L-sampler method will be used instead of the M-sampler method with a probability of 0.5. The `set burn-in iterations' statement specifies 1000 iterations to be performed initially, with one trait locus (if any) unlinked to the marker map. The `check progress' statement instructs the program to print the iteration number every 1000 iterations.

The `compute ibd statistics' statement must be included in the parameter file when running lm_ibdtests. The next line instructs the program to use Spairs and Srobdom to perform the ibd tests. The `set ibd tests' command calls for both normal and permutation tests to be run. The next line is needed since permutation test were requested in the previous line; it specifies how many permutations are to be used in the calculations. In this case, the default (999) is specified; it is recommended that at least 50 permutations are used. The last line in the parameter file is used to specify when to compute scores, the default is every MCMC iteration.