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How to calculate D' and R2 for linkage disequilibrium


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#1 jamestoon1

jamestoon1

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Posted 11 June 2013 - 10:26 AM

Supposed i have 2 polymorphisms, SNPA and SNPB.
Individuals who carry the wildtype genotype for SNPA also carry the wildtype genotype for SNPB.
Individuals who carry the heterozygous genotype for SNPA also carry the heterozygous genotype for SNPB.

Individuals who carry the mutant genotype for SNPA also carry the mutant genotype for SNPB.

It is pretty obvious that the two polymorphisms are in complete linkage disequilibrium, right?
So the D' should equal to 1.

But, how do I calculate that?

I found a web-based software which seems to be easy to use, but I don't know what number should I key in onto each cell --> http://www.oege.org/software/cubex/

Now supposed I have 1000 wildtype, 800 heterozygous and 600 mutants for both polymorphisms, what number shall I put in the cells?

I tried the following (based on the frequencies of my genotypes):
2000---1800---1600
1800---1600---1400
1600---1400---1200

But I got a D' value of -0.011 instead of 1.

Can anyone help?

You may recommend other softwares or simple methods for calculating the D' and r2.

Thanks in advance.

#2 jamestoon1

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Posted 12 June 2013 - 09:33 AM

Nobody answered, but never mind, I already know the answer.
Supposed to fill as follows:

1000---0---0
0---800---0
0---0---600




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