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Linkage score test

We wish to test the null hypothesis of no linkage between the marker and a DS locus , which could be one of several unlinked DS loci, that is, we wish to test

where denotes the recombination fraction between and .

It is easy to show that there is no uniformly most powerful (UMP) test of vs . In most situations, alternatives close to the null hypothesis are hard to detect, thus, it is appropriate to use a test which has as high a power as possible for alternatives close to the null hypothesis. Even if there is no UMP test, we may find a test which is locally most powerful (LMP), i.e. which maximizes the power for alternatives that are close to : the score test. The score test is based on the first non-zero derivative in the Taylor series expansion of the log-likelihood about . In our problem, the first derivative vanishes, so we turn to the second derivative of the log-likelihood with respect to , which yields a test that maximizes the second derivative of the power function at the null. We find the score statistic to be

and reject the null hypothesis of no linkage for large values of .





Simon Cawley
Tue May 26 19:30:26 PDT 1998