linkage user's guide (version 5.2)

4.1 UNKNOWN

UNKNOWN infers possible genotypes and mating combinations for parents with unknown genotypes for ILINK, MLINK and LINKMAP. The following constants must be set prior to compiling the program: 
maxlocus       { MAXIMUM NUMBER OF LOCI }
maxfem         { MAXIMUM NUMBER OF SINGLE LOCUS GENOTYPES FOR A FEMALE }
maxmal         { MAXIMUM NUMBER OF SINGLE LOCUS GENOTYPES FOR A MALE }
maxall         { MAXIMUM NUMBER OF ALLELES AT A SINGLE LOCUS }
maxind         { MAXIMUM NUMBER OF INDIVIDUALS IN ONE PEDIGREE }
maxmarriage    { MAXIMUM NUMBER OF MARRIAGES FOR ONE MALE }

          { BINARY  (FACTOR UNION) SYSTEM }

maxfact        {MAXIMUM NUMBER OF BINARY CODES AT A SINGLE LOCUS}

          { QUANTITATIVE TRAIT }

maxtrait       { MAXIMUM NUMBER OF QUANTIT. FACTORS AT A SINGLE LOCUS }
missval=0.0;   { MISSING VALUES FOR QUANTITATIVE TRAITS }
affall=2;      { ALLELE GIVING AFFVAL FOR QUANT. TRAITS IN MALES, SEXLINK }

          { AFFECTION STATUS }

missaff=0;     { MISSING VALUE FOR AFFECTION STATUS }
affval = 2;    { CODE FOR AFFECTED INDIVIDUAL }
maxliab        { MAXIMUM NUMBER OF LIABILITY CLASSES }

          { OTHERS }

maxn           { MAXIMUM NUMBER OF ITERATED PARAMETERS IN ILINK }
MAXFEM need be no larger than nallele x (nallele+1)/2 where nallele is the actual number of alleles at a locus. MAXMAL can be equal to MAXFEM, even for sex-linked traits without loss of efficiency.

The following constants should not be changed: 

doeliminate = FALSE;     { ELIMINATE SOME ALLELES IN UNKNOWNS }
minfreq = 0.05;          { MINIMUM FREQUENCY FOR ELIMINATION }

UNKNOWN produces IPEDFILE and SPEEDFILE as output files. DATA- FILE and PEDFILE are required as input.

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