13.2 Sample lm_map parameter file

This example parameter file may be found in the `Map' subdirectory of the updated `MORGAN-examples' directory (Aug 22, 2007). An older example is in the `Map' subdirectory of the downloadable `MORGAN-examples' directory.

input pedigree file 'map.ped' input marker data file 'map.marker' input seed file '../sampler.seed' output overwrite seed file '../sampler.seed' select all markers map gender F mark recomb fract .12 .18 map gender M mark recomb fract .10 .20 output maps gender averaged specific limit recomb fracts .01 set EM convergence .2 set SA convergence .001 set ascent iterations 100 set LRT stat iterations 500 set curvature iterations 500 set gradient iterations 10 set mark 1 2 3 freqs .25 .25 .25 .25 use 100 sequential imputation realizations for setup sample by scan set L-sampler probability .8 set burn-in iterations 100 set MC iterations 50

Statements `output maps gender averaged specific' and `use MCEM only for maximization' tell lm_map to find the MLE for both sex-averaged and sex-specific maps, and that only the MCEM algorithm should be used for maximization.

Statements `map gender F marker recombination fraction .12 .18' and `map gender M marker recombination fraction .10 .20' set the initial female and male maps for MCEM by specifying consecutive intermarker recombination fractions of the map for each gender. The initial sex-averaged map is simply the average of the two sex-specific maps.

Statement `use 100 sequential imputation realizations for setup' tells lm_map to sample 100 inheritance patterns from an approximate posterior distribution to find an initial inheritance pattern to seed the Markov chain.

Statements `sample by scan' and `set L-sampler probability .8' tell lm_map that 80% of the sampled inheritance patterns should derive from updates at each locus, whereas 20% should derive from updates at each meiosis.

Statement `set MC iterations 50' sets the initial MCEM sample size, which is then doubled for each successive step of the algorithm.

Statement `limit EM iterations 10' puts an upper bound on the number of MCEM steps.

With statement `set EM convergence .01', the MCEM algorithm stops if all recombination fraction updates are within 0.01 of their previous values.

Statement `limit recombination fractions .01' provides a lower bound for the estimated recombination fraction for any interval in the map.

With statement `set map estimation model with no mistyping', lm_map assumes that the genotypes in `map.dat' are observed without error.

Statement `set markers 1 2 3 4 frequencies .25 .25 .25 .25' tells lm_map that the marker data in `map.dat' correspond to four markers (labelled 1 - 4), and that each marker has four equi-frequent allelels (labelled 1 - 4).

Statement `select all markers' extracts a subset of the marker data for analysis. In this case, the extracted subset is also the complete set, since 'all' markers have been selected.