The parameter file is a specially formatted file that is used by all the disease gene mapping programs. It contains the disease model, marker information, and mapping information. Please see the documentation posted at Rockefeller that describes parameters.

Before you get started with this procedure, take a look at your recode.dat file. It should look something like the example below:

In the first row of this file: 3 is the marker type (all microsatellite markers and SNPs will use 3 as their marker type); the second number is the number of alleles in in the corresponding genotypes file for that marker. In the second row: Each decimal number is the frequency of each allele for that particular marker. Every two rows represents the information for one marker.

3 4 0.08333 0.02778 0.16667 0.72222 3 6 0.05882 0.05882 0.29412 0.35294 0.17647 0.05882 3 5 0.08333 0.02778 0.16667 0.72222

Now you are ready to create the datain.dat file. This file will be used to analyse your pedigree data. There is an interactive program (preplink) that can generate a datain.dat file, but it was originally written for DOS and its user-interface is awful. Instead just use "copy-and-paste" to modify an old datain.dat file. Use a text editor to create the file. Copy and paste the text in the right side of the table (below) into your document:

Replace all the #'s with your own information

The words following each << are comments. Line 1: The first # is the total no. of markers PLUS the no. of disease loci. The second # is program code (5= MLINK). Line 3: Integers representing each locus. 1 is the disease locus, followed by increasing consecutive integers for each marker (2, 3, 4, 5, etc.) Line 6: You may set penetrances according to the disease. Lines 7 - 12 correspond to recode.dat. Line 14: map information specific to your case.

# 0 0 # << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM 0 0.0 0.0 0 << MUT LOCUS, MUT MALE, MUT FEM, HAP FREQ (IF 1) 1 # # # 1 2 << AFFECTION, NO. OF ALLELES 0.99000 0.01000 << GENE FREQUENCIES 1 << NO. OF LIABILITY CLASSES 0 0.95 0.95 << PENETRANCES 3 # << ALLELE NUMBERS, NO. OF ALLELES #.##### #.##### #.##### #.##### << GENE FREQUENCIES 3 # << ALLELE NUMBERS, NO. OF ALLELES #.##### #.##### #.##### #.##### << GENE FREQUENCIES 3 # << ALLELE NUMBERS, NO. OF ALLELES #.##### #.##### #.##### #.##### << GENE FREQUENCIES 0 0 << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2) 0.1000 0.1000 0.1000 << RECOMBINATION VALUES 1 0.05 0.35 << REC VARIED, INCREMENT, FINISHING VALUE

You may add the marker's name to the datain.dat file. To do this, put a space after your entry for NO. OF ALLELES and then type: # Markername. This is a good way to record which markers the parameter file is covering, since they are not listed in the *.pre. Genehunter identifies marker names in this format, and will print them in some of its output, but none of the other linkage programs we use do.

For the example pedigree1.rec, the datain.dat file would look like this if the first marker's name is D7S550:

4 0 0 3 << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM 0 0.0 0.0 0 << MUT LOCUS, MUT MALE, MUT FEM, HAP FREQ (IF 1) 1 2 3 4 1 2 << AFFECTION, NO. OF ALLELES 0.99000 0.01000 << GENE FREQUENCIES 1 << NO. OF LIABILITY CLASSES 0 0.95 0.95 << PENETRANCES 3 4 # D7S550 << ALLELE NUMBERS, NO. OF ALLELES 0.08333 0.02778 0.16667 0.72222 << GENE FREQUENCIES 3 6 << ALLELE NUMBERS, NO. OF ALLELES 0.05882 0.05882 0.29412 0.35294 0.17647 0.05882 << GENE FREQUENCIES 3 5 << ALLELE NUMBERS, NO. OF ALLELES 0.08333 0.02778 0.16667 0.72222 << GENE FREQUENCIES 0 0 << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2) 0.1000 0.1000 0.1000 << RECOMBINATION VALUES 1 0.05 0.35 << REC VARIED, INCREMENT, FINISHING VALUE

Save your document as datain.dat Now your data is finally ready for analysis!
Next Step: Run linkage analysis program(s)