Makedata

Description

Makedata program is used to create simple LINKAGE format locus files (data file). More complex locus files can be created with preplink.

Usage

Command is:

    makedata

Makedata asks few basic questions

• Number of markers in pedigree file
• Autosomal or sexlinked data
• Frequency of disease allele
• Liability classes
• Maximum number of alleles at any locus
• Map (optional)

Example

    % makedata

    Makedata 1.4 (06/17/1999). This program creates data files for linkage
    analysis. Made by Tero Juntunen

    MAX liability classes       10
    MAX allele in one loci      50
    MAX loci in one chromosome  500

    How many marker loci?
    2
    Is this set of markers?
    (1) Autosomal
    (2) Sexlinked
    1
    What is the assumed frequecy of the disease allele?
    0.02
    How many liability classes?
    1
    Please enter penetrances for liability class 1.
    P(Aff|DD)   P(Aff|D+)   P(Aff|++)
    0.9 0.9 0.0024
    What is the largest number of alleles at any markers?
    10
    Do you want to specify recombination fraction between markers?
    (0=No, 1=Yes, 2=AUTOSCAN option)
    0

    indata.dat created! Run downfreq to eliminate alleles
    and calculate correct allele frequences.

    %

and indata.dat file looks like:

    3 0 0 5
    0 0.0 0.0 0
    1 2 3 
    1 2
    0.980000 0.020000
    1
    0.002400 0.900000 0.900000
    3 10
    0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 
    3 10
    0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 
    0 0
    0.500 0.10000 
    1 0.1 0.45

After this DOWNFREQ is used to estimate correct allele frequencies. See locus file for more info.

Author

Tero Hiekkalinna

References

Documentation

Webpage