I am working with a sex linked disease. It is 100% penetrant in the males and
one can observer carrier status in the females. So in my linkage runs I am
running it as a sex linked disease and I am calling the carrier females
affected and affected males affected. Is that the correct approach? Or should
I call the females unaffected? Below is the preplink file, and I am running
ilink:
8 0 1 5 << 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 5 6 7 8
1 2 << AFFECTION, NO. OF ALLELES
0.990000 0.010000 << GENE FREQUENCIES
1 << NO. OF LIABILITY CLASSES
0 1.0000 1.0000
0 1.0000 << PENETRANCES
3 4 << ALLELE NUMBERS, NO. OF ALLELES
0.076920 0.461540 0.230770 0.230770 << GENE FREQUENCIES
3 3 << ALLELE NUMBERS, NO. OF ALLELES
0.153840 0.461540 0.384610 << GENE FREQUENCIES
3 6 << ALLELE NUMBERS, NO. OF ALLELES
0.083330 0.250000 0.250000 0.166670 0.166670 0.083330 << GENE FREQUENCIES
3 5 << ALLELE NUMBERS, NO. OF ALLELES
0.166670 0.333330 0.083330 0.250000 0.166670 << GENE FREQUENCIES
3 8 << ALLELE NUMBERS, NO. OF ALLELES
0.230770 0.076920 0.153840 0.230770 0.076920 0.076920 0.076920 0.076920 <<
GENE FREQUENCIES
3 6 << ALLELE NUMBERS, NO. OF ALLELES
0.076920 0.153840 0.230770 0.230770 0.230770 0.153840 << GENE FREQUENCIES
3 7 << ALLELE NUMBERS, NO. OF ALLELES
0.071430 0.214290 0.071430 0.285710 0.214290 0.071430 0.071430 << GENE
FREQUENCIES
0 0 << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2)
0.1000 0.1000 0.1000 0.1000 0.1000 0.1000 0.1000 << RECOMBINATION VALUES
1 0.10000 0.45000 << REC VARIED, INCREMENT, FINISHING VALUE
The weird thing is that I am getting a lodscore that is reasonable, since I am
told it is linked to this locus (Am I biased or what!). However, I am getting
thetas of 0.999 or so with my highest lodscores. So I was thinking that possibly
this is a result of the sex linked disease question.
Any help or insight is appreciated!
Thanks!
