9.4 Sample lm_pval parameter file

Files for lm_pval may be found in the `TraitTests' subdirectory of `MORGAN_Examples'. The parameter file, `ped73_pval.par' is similar to the parameter file used for lm_auto. An abbreviated version of `ped73_pval.par' is given below:

input pedigree file '../ped73.ped' set component 1 affected individuals 302 307 406 407 408 411 414 416 505 507 508 511 512 513 514 516 601 602 set component 2 affected individuals 1301 1302 1304 set component 3 affected individuals 2301 2302 2306 2307 2308 2305 #input pedigree record trait 1 integer 4 #set affected individuals trait 1 input seed file '../sampler.seed' input marker data file '../ped73.marker.missing' select all markers set L-sampler probability 0.2 set MC iterations 2000

For lm_pval, markers are selected, but no trait locus is selected. Therefore, no `map trait marker' statements are included and the trait locus is not included in the `select' statement. The file `ped73.marker.missing' contains the marker map and genotypes, and is accessed by the statement `input marker data file'. Pedigree members affected with the disease must be specified when using lm_pval. Affected individuals may be specified explicitly or determined by using trait data. In the above example, the three `set component [] affected individuals' statements explicitly name each affected individual for each component. Below these three statements are two commented out statements, which can be used instead of the `set component [] affected individuals' statements to specify affected individuals based on trait data. The first of these statements, `set affected individuals trait 1', instructs the program to determine the affected individuals by using the trait data for trait 1 in the pedigree file. Recall that the second commented out statement, `input pedigree record traits', is needed to define the correspondence between trait numbers and integers in the pedigree record, so that the program knows where to find the desired trait data. See the parameter file for further instruction on how to implement the two methods for specifying the affected individuals.