Pairwise LD calculation for probabilistic data

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a.grotenhuis
GenABEL suite user
GenABEL suite user
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Joined: Wed Dec 21, 2011 9:42 am

Pairwise LD calculation for probabilistic data

Postby a.grotenhuis » Wed Jul 09, 2014 6:36 am

I wonder is there a way to calculate pairwise LD (R2) for probabilistic SNP data, e.g. for LD pruning? Does ProbABEL or any other statistical package offer opportunities for calculation? Or are there currently only ways to calculate pairwise LD for called genotype data (0,1,2)?

Thanks.

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