Dean Flanders (dean at birch.med.umn.edu) wrote:
: 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!
Dear Dean,
The result you got is due to the starting theta values
of your ilink run.
You should first of all run 2 point mlink
with all couples disease-marker and marker-marker.
Then set the starting thetas values to or close to
the thetas corresponding to Z (2 point) max.
You may call carrier females affected, it is surely
not the cause of your problem.
Hope it helps.
Regards
Lucien Bachner
P.S : The real cause of your result is that ilink has converged
to a local maximum because of your starting values.
--
Lucien Bachner
Infobiogen
bachner at infobiogen.frlinkage at infobiogen.fr
