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R implementation of the Trio Correlation test.
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Epistasis plays a significant role in the genetic architecture of many complex phenotypes in model organisms. To date, there have been very few interactions replicated in human studies due in part to the multiple hypothesis burden implicit in genome-wide tests of epistasis. Therefore, it is of paramount importance to develop the most powerful tests possible for detecting interactions. In this work we develop a new gene-gene interaction test for use in trio studies called the trio correlation (TC) test. The TC test computes the expected joint distribution of marker pairs in offspring conditional on parental genotypes. This distribution is then incorporated into a standard one degree of freedom correlation test of interaction. This directory contains the R implementation of the proposed test.

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