SIM(1)                  APM GENETICS PROGRAMS                  SIM(1)

NAME

     sim - simulate pedigrees using apm program output

DESCRIPTION

    This program simulates pedigrees by generating random genotypes
    for each member over a number of iterations. It computes the
    statistic over all families for each locus and for each iteration,
    and then it computes the mean and variance of these statistics.

    The program has also been modified to exclude parent-child pairs
    from the APM statistic. It has been found that this yields
    greater power in detecting linkage, and since parent-child
    pairs are excluded in the apm program, they must be excluded here
    as well.

INPUT FILE FORMATS

    The output files out1.dat, outsqr.dat, and out1p.dat produced
    by apm are intended for use with the sim program.
    The formats of all of these files are the same (they differ in
    the function used to weight the allele frequencies: f(p) = 1,
    f(p) = 1/sqrt(p), f(p) = 1/p, respectively):

    <magic number>
    <number of pedigrees>   <number of loci>
    <number of alleles for locus #1>   <name of locus #1>
    <frequency of allele #1>
    <frequency of allele #2>
    .
    .
    .
    <number of alleles for locus #2>   <name of locus #2>
    .
    .
    .
    <title of pedigree #1>
    <number of members>   <number of affecteds>   <number of loci>
    <list of mothers>
    <list of fathers>
    <locus number>   <number of affecteds at this locus>
    <affected #1>
    <affected #2>
    .
    .
    .
    <cumulative mean>   <cumulative variance>
    <locus number>
    .
    .
    .
    <title of pedigree #2>
    .
    .
    .
    <statistic for first locus> <p-value>
    <statistic for second locus> <p-value>
    .
    .
    .

OUTPUT FILE FORMATS

    There is one output file for each locus, named tstat<n>.out
    (where <n> is the locus number). Each file contains the
    simulated statistics for each iteration - useful if you
    need them for input to a statistics package.

    There is also one output file, sim.out, which is appended
    each time you run sim. It contains all the results of the
    runs that you normally see at the standard output.

BUGS

    There aren't any that I know of.

REFERENCES

    See the accompanying REFERENCES file.


APM Release 2.0  Last change: 5 Jul 1993