Re: [R] Incomplete Trio in TDT analysis

From: Farrel Buchinsky <fbuchins_at_wpahs.org>
Date: Mon 08 May 2006 - 11:24:36 EST


 Steve Buysek Wrote

Using only informative incomplete trios and dropping others turns out to bias the TDT (Curtis & Sham 95). There are a variety of modifications to handle case-parent trios, starting (I think) with Weinberg's 1999 paper that uses the EM algorithm and a likelihood-ratio test. I don't know of any of these methods that are implemented in R. Perhaps they are in the package that you are using but forgot to name.
Steve Buyske

My response:

I read through some of literature on the topic. The latest publication appears to be
Guo CY, DeStefano AL, Lunetta KL, Dupuis J, Cupples LA. Expectation maximization algorithm based haplotype relative risk (EM-HRR): test of linkage disequilibrium using incomplete case-parents trios. Hum Hered 2005;59(3):125-35.

In it the authors make statements that lead me to believe that it would meet my needs better than the EM likelihood-ratio test. [I am not equipped to either agree or disagree with their assertion] The package that I was using is dgc.genetics and as far as I know is the only tdt implementation in R.

Farrel Buchinsky



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