Abstract
Composite likelihood methods have become very popular for the analysis of large-scale genomic data sets because of the computational intractability of the basic coalescent process and its generalizations: It is virtually impossible to calculate the likelihood of an observed data set spanning a large chromosomal region without using approximate or heuristic methods. Composite likelihood methods are approximate methods and, in the present article, assume the likelihood is written as a product of likelihoods, one for each of a number of smaller regions that together make up the whole region from which data is collected. A very general framework for neutral coalescent models is presented and discussed. The framework comprises many of the most popular coalescent models that are currently used for analysis of genetic data. Assume data is collected from a series of consecutive regions of equal size. Then it is shown that the observed data forms a stationary, ergodic process. General conditions are given under which the maximum composite estimator of the parameters describing the model (e.g. mutation rates, demographic parameters and the recombination rate) is a consistent estimator as the number of regions tends to infinity.
| Original language | English |
|---|---|
| Journal | Journal of Mathematical Biology |
| Volume | 53 |
| Issue number | 5 |
| Pages (from-to) | 821-841 |
| Number of pages | 21 |
| ISSN | 0303-6812 |
| DOIs | |
| Publication status | Published - 1 Nov 2006 |
| Externally published | Yes |
Keywords
- Coalescent theory
- Composite likelihood
- Consistency
- Estimator
- Genomic data