 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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