1 ! number of trait loci (I8) [you will have just one] traitnam 3 ! trait locus name (A8), number of liability classes (I8) 101 0.90 0.90 0.10 ! liab. class (I8), 3 penetrances (3F8.5) 201 0.10 0.10 0.90 ! liab. class (I8), 3 penetrances (3F8.5) 102 0.95 0.95 0.05 ! liab. class (I8), 3 penetrances (3F8.5) 202 0.05 0.05 0.95 ! liab. class (I8), 3 penetrances (3F8.5) 103 0.99 0.99 0.00 ! liab. class (I8), 3 penetrances (3F8.5) 203 0.01 0.01 1.00 ! liab. class (I8), 3 penetrances (3F8.5) _____________________________<bottom of file>______________________________
Please see the penetrance format file for a full description of this file format.
The comments, that appear from the '!' onwards, are of course disregarded and optional.
In this example, an affected person in liability class #1 should, in the pedigree data file, have the value 201 in their first quantitative variable, i.e., the first piece of data after the last marker genotype for that person. Then, for example, the penetrance for the 2/2 genotype at the trait locus for that person will be 0.90 .
Adding liability classes to the pedigree may require one to adjust the format listing on the second line of the pedigree data file to indicate that there is this additional data item immediately after the last marker genotype. Recall, however, that in this format listing all variables must be read in as character strings, that is, using the 'A' edit descriptor, for example, using A8.
One last reminder, since the liability class information is in the first quantitative variable, be sure and set batch item #18 to (at least) 1. This batch item tells SimWalk2 how many quantitative variables need to be read in.