>datain.dat:
>--------
> 4 0 0 1 << no loci, risk locus, sexlinked(if 1)
> 0 0.0 0.0 0 << mut locus, mut rate, haplotype freq(if 1)
> 1 2 3 4 << order of loci
>> 1 2 << affectation, # alleles [CHED]
> 9.9900000000E-01 1.0000000000E-03 << gene freqs
> 1 << number of liability classes
> 0.000 1.000 1.000 << genotype penetrances
>
Because the disease allele has a frequency of 0.001, there is a small
though not infinitesimal probability for there to be two different
disease alleles entering the pedigree, one segregating in one branch
and another segregating in the other branch. Thus your results are
just what I would expect. I would predict that as you decrease the
frequency of the disease allele, so the lod score at zero will
decrease, eventually approaching minus infinity as the allele
frequency becomes vanishingly small. I would also predict that the lod
score at small non-zero values for theta will change very little when
you do this, for reasons which I hope are obvious.
