9.2 Sample lm_auto parameter file

Files for lm_auto may be found in the `IBD' subdirectory of `MORGAN_Examples'. Below is an annotated parameter file, `jv_rep_auto.par', for use with lm_auto:

input pedigree file 'jv_rep.ped' input seed file '../sampler.seed' select all markers traits 1 map gender F markers distances 25.5 25.5 25.5 25.5 map gender M markers distances 11.2 45.8 11.2 45.8 map gender F trait 1 marker 2 distances 12.8 map gender M trait 1 marker 2 distances 5.8 set markers 1 2 3 4 freqs .2 .2 .4 .1 .06 .04 set markers 5 freqs .3 .2 .3 .1 set trait 1 freqs .95 .05 set marker data 5 333 1 3 1 3 1 3 1 3 1 3 331 3 4 3 4 3 4 3 4 3 4 334 2 3 2 3 2 3 2 3 2 3 431 3 4 3 4 3 4 3 4 3 4 531 3 3 3 3 3 3 3 3 3 3 343 1 3 1 3 1 3 1 3 1 3 341 3 5 3 5 3 5 0 0 3 3 344 4 6 4 6 4 6 2 4 2 4 441 3 4 3 4 0 0 3 4 3 4 541 3 3 3 3 3 3 3 3 3 3 set window patterns 0 4 set locus window 3 set component 1 proband gametes 531 1 531 0 331 0 333 1 set component 2 proband gametes 541 1 541 0 set L-sampler probability 0.2 set MC iterations 2000

The pedigree file specified here, `jv_rep.ped', is a 30-member, two-component pedigree in which the final individuals (named 531 and 541) have trait value `4'. All other individuals in the file have trait value `0'. Because the trait type is not specified in the parameter file via a `set trait data' statement, the trait type is assumed to be genotypic. This means that the trait locus genotype can be inferred from the trait value, i.e., there are three distinct trait values, each corresponding to a distinct genotype at the trait locus. The trait values are specified in the parameter file and are coded as `1', `3', `4' or `0', corresponding to trait locus genotypes of `1 1', `1 2' (or `2 1'), `2 2' or `missing', respectively. Unless otherwise specified, the trait value is listed after names and gender in the pedigree file.

The `map' statements specify the marker map and trait position in terms of genetic distances (centiMorgan). In this example there are five markers with sex--specific maps. The trait locus is between markers 2 and 3, with genetic distances given in terms of the marker to its left, which is marker 2. See genedrop mapping model parameters. The first four markers each have six alleles (labeled 1--6) with frequencies 0.2, 0.2, 0.4, 0.1, 0.06 and 0.04. The fifth marker has four alleles with frequencies 0.3, 0.2, 0.3 and 0.1. The trait locus has two alleles; alleles `1' and `2' have frequencies 0.95 and 0.05, respectively. The `select' statement is analogous to genedrop's `simulate' statement (see genedrop computing requests).

Following the `set marker data' statement are genotype data for typed individuals. The number of markers, 5, is given in the `set marker data' statement. Alternatively, genotype data could be provided to lm_auto in a separate file, specified using an `input marker data file' statement.

`set proband gametes' is the key statement for lm_auto. With it, the user specifies which haplotypes are to be scored with ibd probabilities. The statement requires a list of individual IDs and an indicator of paternal (1) or maternal (0) haplotype. For example, `531 1' refers to the paternal (1) haplotype of individual 531. In the example, the statement requests scoring both haplotypes of 531, the maternal(0) haplotype of 331 and the paternal (1) haplotype of 333. See ibddrop statements, for more discussion of the `set proband gametes' statement.

The `set window patterns' and `set locus window' statements go together. They instruct lm_auto to compute probabilities that the gametes named in the `set proband gametes' statement have a particular ibd pattern (also called state) across several loci. In this case, we are interested in patterns `0' and/or `4' across windows of three markers at a time. Recall the output of the ibddrop program generated when using the parameter file, `ibd.par'. In the section of the program output headed "Probabilities of IBD patterns", each of the ibd patterns listed in the left-most column is associated with a label in the right-most column. The `set window patterns' statement expects one or more of these labels, instructing lm_auto to calculate probabilities of the associated pattern(s). The `set locus window' statement specifies the number of loci to be examined simultaneously, in this case 3. In the example here, window patterns `0' and `4' are requested, which correspond to ibd patterns `1 1 1 1' and `1 1 2 2', respectively. In other words, we are interested in the probability that all four of the gametes named in the `set proband gametes' statement are ibd across 3-locus windows or that the first two gametes (maternal and paternal haplotypes of individual 531) are ibd and the second two gametes (maternal haplotype of individual 331 and paternal haplotype of individual 333) are ibd, but the pairs are not ibd with one another.

As with all of MORGAN's MCMC-based programs, the user can specify the desired number of MC iterations using the `set MC iterations' statement, the desired number of burn-in iterations using `set burn-in iterations', and the probability that the L-sampler is selected instead of the M-sampler using `set L-sampler probability'. In this example, 2000 sampling iterations are to be performed, using the L-sampler 20 percent of the time. These iterations are preceded by burn-in iterations. Because the number of burn-in iterations is not specified, lm_auto will use the default value of 10 percent of the number of main iterations. In practice, one would run the MCMC sampler much longer than 2000 iterations. This is just for demonstration.