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Bgim - Maximum Likelihood Estimation Primer
Bgim - Maximum Likelihood Estimation Primer
(MLE)
The test for linkage is simply the test of whether the recombination fraction (
) is 0.5 (the null hypothesis of no linkage) or less than 0.5 (the alternative
hypothesis of linkage).
You might have noticed a striking similarity to the coin-flipping example here.
The good news is that the analysis is virtually identical. Note that, in real life, we
would not expect to observe fully informative gametes for all pedigrees, and
more complex methods have to fill in the gaps, but the principles are much the
same.
Since each gamete has probability of being recombinant and probability (1-
) of being non-recombinant, the likelihood function is
Note : strictly speaking, the likelihood is proportional to this quantity rather than equal to
it - notice that the constant part of the binomial formula has been dropped.
The null hypothesis of no linkage implies =0.5, so the value of the log-
likelihood function is
for biological reasons Under the alternative of linkage, the maximum log-
likelihood is
when R>(N/2).
The likelihood ratio statistic 2(lnLA - lnL0) provides a direct test for linkage.
Note: this likelihood ratio statistics is distributed as a 50:50 mixture of chi-squared with
one degree of freedom and point probability mass of 0. In this way, a one-tailed test of
linkage is provided.
An Example
27 recombinants
from 139 fully informative gametes