APMMULT(1)              APM GENETICS PROGRAMS               APMMULT(1)


NAME

    apmmult - compute the multiple-locus APM statistic (from MULT files)

DESCRIPTION

    This program is designed to efficiently compute the multilocus APM
    statistic for a number of pedigrees over a number of marker loci.
    It is capable of storing the results of kinship calculations
    internally, greatly speeding up computations.

    Internally storing the kinship values requires large amounts of
    memory. In order that this program may be used on systems with limited
    memory, a scheme to limit the amount of information stored has been
    employed. Unfortunately, some pascal compilers halt with an error
    when a new() can't allocate memory; this makes the memory limiting
    very necessary but of limited use. Users with those compilers may
    have to set a very small limit.

    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.

    At some time in the future, this program will probably be
    combined with apm.

LIMITS

    As distributed, the program can handle up to 50 families with
    up to 50 members each and 20 marker loci of up to 50 alleles each.
    Pedigree titles can be up to 80 characters long.

    The maximum number of families, members, loci, and alleles can
    all be changed by altering constants at the beginning of the
    program. There are other constants that depend on these, as
    described in the comments, and they should be changed as well.

    The problem, of course, with just making these numbers huge
    is that some compilers have limits on the amount of memory used
    for variables in each block.

INPUT FILE FORMATS

    All affecteds must be typed at ALL markers. The program takes MULT
    format APM files (see the INTRO file for more details). The file
    format looks like this:

     <number of pedigrees>   <number of loci>
     <number of alleles at locus #1>   <name of locus #1>
     <list of allele frequencies for locus #1>
     <number of alleles at locus #2>   <name of locus #2>
     .
     .
     .
     <title of pedigree #1>
     <number of members>  <number of affecteds>
     <list of mothers>
     <list of fathers>
     <affected #1> <genotype at locus #1> <genotype at locus #2> ...
     <affected #2> <genotype at locus #1> <genotype at locus #2> ...
     .
     .
     .
     <title of pedigree #2>
     .
     .
     .
     
    Here is a real example data file:

          2   3
       3   ACK1
    0.450  0.300  0.250
       3   ACK2
    0.550  0.200  0.250
       2   ACK3
    0.465   0.535
       TESTPED1
          15   3
       0 0 2 2 2 0 0 0 5 5 5 7 12 12 12
       0 0 1 1 1 0 0 0 6 6 6 8 11 11 11
     4    2 2   2 2   1 2
     10   3 3   1 3   2 2
     13   3 2   1 1   1 2
       TESTPED2
          8   2   1
       0 0 1 1 1 0 6 6
       0 0 2 2 2 0 5 5
     4    1 3   1 1   2 2
     7    2 3   3 3   1 1


OUTPUT FILE FORMATS

    The output files out1.dat, outsqr.dat, and out1p.dat are
    intended for use with the simmult 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>
    <list of mothers>
    <list of fathers>
    <affected #1>
    <affected #2>
    .
    .
    .
    <list of cumulative means and variances for the loci>
    <list of observed X values for all loci>  <total multilocus variance>
    <title of pedigree #2>
    .
    .
    .
    
    The output file out1.dat for the above pedigree file looks like
    this:

          11
           2         3
           3   ACK1   
     0.45000
     0.30000
     0.25000
           3   ACK2   
     0.55000
     0.20000
     0.25000
           2   ACK3   
     0.46500
     0.53500
     TESTPED1
              15             3
     0   0   2   2   2   0   0   0   5   5   5   7  12  12  12
     0   0   1   1   1   0   0   0   6   6   6   8  11  11  11
     4
    10
    13
               1.26656             0.27363             1.40094             0.35872
             1.66283             0.25792
               1.00000             0.50000             1.50000             0.89705
     TESTPED2
               8             2
     0   0   1   1   1   0   6   6
     0   0   2   2   2   0   5   5
     4
     7
               0.43562             0.05997             0.47938             0.06961
             0.56464             0.05909
               0.25000             0.00000             0.00000             0.19026

    In addition to those three files, a summary file is produced,
    named 'table.out'. It contains the locus information, the statistics
    and their p-values for all families, and the overall statistics
    and their p-values. The format is obvious; the example file to
    go with the above pedigree file is not included here as it is
    rather lengthy.

    Finally, there is one other output file, apmmult.out. This file
    consists of lines of the following format:

    <number identifying pedigree (1, 2, 3, ...)>
    <multilocus covariance, observed X, mean, variance, and total variance>

    (that's all on one line).

BUGS

    Please let us know if you find any!

REFERENCES

    See the accompanying REFERENCES file.


APM Release 2.0  Last change: 5 Jul 1993