LINKMEND     

   This file converts Linkage files to Mendel files.
   The Linkage datafiles must have the names indicated
   below and must be in the correct Linkage format.

   Input:
     datafile.dat -> Linkage data file (locus info)
     pedfile.dat  -> Linkage pedigree file 

   Output:
     locus.dat -> MENDEL locus data file
     pedm.dat  -> MENDEL pedigree data file
     batch.dat -> MENDEL batch file suitable for estimating allele frequencies
		  using the USERM13 program.


   At present, there is no automatic conversion of
   the penetrance table for affection status loci.

   Also, LinkMend does not handle pedigrees with loops.

********************************
| Daniel E. Weeks              | 
| Department of Human Genetics |  Internet: 
| University of Pittsburgh     |    dweeks@watson.hgen.pitt.edu
| Crabtree Hall, Room A310     |
| 130 DeSoto Street            |  Bitnet:
| Pittsburgh, PA 15261         |    weeks@pittvms.bitnet
|                              |
| (412) 624-3066               |
| FAX: (412) 624-3020          |
********************************


Example:
  The LINKAGE datafile.dat below contains two types of
  affection status loci, one with one liability class and
  one with 3 liability classes.  In addition, it contains
  a numbered allele system and a binary factor locus.  

LINKAGE datafile.dat:
 4 0 0 5  << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM
 0 0.0 0.0 0  << MUT LOCUS, MUT RATE, HAPLOTYPE FREQUENCIES (IF 1)
  1  2  3  4
1   2  << AFFECTION, NO. OF ALLELES
 0.990000 0.010000   << GENE FREQUENCIES
 1 << NO. OF LIABILITY CLASSES
 0.0000 0.0000 1.0000 << PENETRANCES
1   2  << AFFECTION, NO. OF ALLELES
 0.999000 0.001000   << GENE FREQUENCIES
 3 << NO. OF LIABILITY CLASSES
 0.0500 0.5000 0.5000
 0.0000 0.0000 1.0000
 0.0000 0.9500 0.9500 << PENETRANCES
3   2  << ALLELE NUMBERS, NO. OF ALLELES
 0.750000 0.250000   << GENE FREQUENCIES
2   2  << BINARY FACTORS, NO. OF ALLELES
 0.500000 0.500000   << GENE FREQUENCIES
 2 << NO. OF FACTORS
 1 0
 0 1  << ALLELIC CODES
 0 0  << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2)
 0.10000 0.10000 0.10000 << RECOMBINATION VALUES
 1 0.10000 0.45000 << REC VARIED, INCREMENT, FINISHING VALUE

LINKAGE pedfile.dat:
1 1 0 0 3 0 0 1 1  0  0 1  1 2  0 1  Ped: 1  Per: 1
1 2 0 0 3 0 0 2 0  1  2 1  2 2  1 1  Ped: 1  Per: 2
1 3 1 2 0 4 4 1 0  2  2 2  1 2  1 1  Ped: 1  Per: 3
1 4 1 2 0 0 0 2 0  2  2 3  2 2  0 1  Ped: 1  Per: 4

The above datafile.dat and pedfile.dat get converted
to the following locus.dat and pedm.dat.  Note how
the liability classes are re-coded in a consistent
manner, but the exact liability classes must be coded
into the APEN subroutine of USERM*.FOR of the MENDEL
package.

MENDEL locus.dat:
       1AUTOSOME 2 2 <= Locus,Type,# Alleles,# Phenotypes
       1 0.99000     <= Allele, Frequency
       2 0.01000     <= Allele, Frequency
1        2 Phenotype 1, 2 genotypes 0.00 0.00 1.00<=Penetrances
1/1               Genotype 1
1/2               Genotype 2
2        1 Phenotype 2, 1 genotype 
2/2               Genotype 1
       2AUTOSOME 2 6 <= Locus,Type,# Alleles,# Phenotypes
       1 0.99900     <= Allele, Frequency
       2 0.00100     <= Allele, Frequency
 1  1    3 # Genotypes 0.95 0.50 0.50<= Penetrances
  1/  1
  1/  2
  2/  2
 1  2    2 # Genotypes 1.00 1.00 0.00<= Penetrances
  1/  1
  1/  2
 1  3    3 # Genotypes 1.00 0.05 0.05<= Penetrances
  1/  1
  1/  2
  2/  2
 2  1    3 # Genotypes 0.05 0.50 0.50<= Penetrances
  1/  1
  1/  2
  2/  2
 2  2    1 # Genotypes 0.00 0.00 1.00<= Penetrances
  2/  2
 2  3    2 # Genotypes 0.00 0.95 0.95<= Penetrances
  1/  2
  2/  2
       3AUTOSOME 2 0 <= Locus,Type,# Alleles,# Phenotypes
       1 0.75000     <= Allele, Frequency
       2 0.25000     <= Allele, Frequency
       4AUTOSOME 2 3 <= Locus,Type,# Alleles,# Phenotypes
10       0.50000     <= Allele, Frequency
01       0.50000     <= Allele, Frequency
10       1  <= phenotype
10/10
11       1  <= phenotype
10/01
01       1  <= phenotype
01/01

MENDEL pedm.dat:
(I5,1x,A8)
(3A5,1X,2A1,(T19,3(A8),:))
    4        1
    1           M                   1/  2 
                  01     
    2           F   1       2   1   2/  2 
                  11     
    3    1    2 M   2       2   2   1/  2 
                  11     
    4    1    2 F   2       2   3   2/  2 
                  01