9.4 Sample lm_pval parameter file

Files for lm_pval may be found in the `Nonparametric' subdirectory of `MORGAN_Examples'. The parameter file, `ped73_pval.par' is similar to the parameter file used for lm_auto.

input pedigree file '../ped73_ph.ped' input pedigree record trait 1 integer 3 set component 1 affected individuals 410 511 512 set component 2 affected individuals 1301 1302 1303 1305 input seed file '../sampler.seed' input marker data file '../ped73.marker.missing' select all markers set L-sampler probability 0.2 ## recommended number of iterations is on the order of 10^5 set MC iterations 2000

For lm_pval, markers but no trait locus are selected. Therefore, we do not need `map trait marker' statements and we do not include the trait locus in the `select' statement. The marker map and genotypes are in a separate file `ped73.marker.missing', included using the statement `input marker data file'. lm_pval requires identification of pedigree members affected with the disease; this is done using the `set affected individuals' statement.