5.3 Running genedrop examples and sample output

Two examples are available under the subdirectory `Simulation/'. The commands to run these examples are similar to the following:

genedrop ped73_gdrop.par ped ../ped73.ped seed ../marker.seed oped ../ped73_gdrop_simu.oped

Upon running the genedrop example, notice (but do not worry about) the appearance of a warning message on the screen: `Overrides previous statement of same type (W)'. The warning was triggered by the specification of `seeds' as both the input and output seed file, without inclusion of `overwrite' in the `output seed file' statement. When an overwrite is not requested, MORGAN appends the new output seeds to the existing file at the end of the run. Thus, at the next run, more than one `set marker seeds' statement exists in the seed file. The program uses only the last `set marker seeds' statement in the file and issues the warning to indicate this to the user. To avoid this warning (and an ever-growing seed file), one can access the seed file from the parameter file as at the beginning of the previous section Sample genedrop parameter file, using the `overwrite' option when outputting the seeds.

Unlike other MORGAN programs, genedrop always creates an output pedigree file, as the function of the program is to simulate marker and trait data. The output file, `ped73_gdrop_simu.dat' here, has the same structure as the input file `ped73.ped', with one individual per record (line), but the output file does not include the parameter statements at the top of the input file and contains additional columns. The first four items are the individual's name, the names of the parents and gender. If no addition output options are set, the next items are the genotypes of the markers (two items per marker) in their order on the chromosomes, and the trait values in the order of trait labels.

Since `output pedigree record trait latent variables' was included in the parameter file, the output file contains four additional columns preceding the trait value. They are: trait locus genotype (2 columns), additive component of the trait value and residual component of the trait value. In this example, everyone has a `0.000' in the additive component column, as we set the additive variance to zero in the parameter file.

Because `output pedigree record founder gene labels' is set, the founder gene lables (FGLs) for markers precede the marker genotypes and the trait FGLs precede the trait locus genotypes (only if latent variables are requested, as in this example).

Also, the `output pedigree record unobserved variables' statement is included in `gdrop.par', so an observed indicator would follow gender in the output pedigree file.