Linkmend

Program to convert Linkage files to Mendel files.

Author: Daniel E. Weeks, Ph.D.

Distribution:

Language:

Pascal

Input:

The Linkage datafiles must have the names indicated below and must be in the correct Linkage format.

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.

hetero.dat -> Counts of informative meioses in the pedigree (for each marker locus).

pen.dat -> Penetrance table for use with a special version of MENDEL which will handle LINKAGE-style liability classes.

 

Note: LinkMend does not handle pedigrees with loops.

 

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

For further questions or comments contact dweeks@pitt.edu.