Module:Bio::PopGen::Statistics
| Pdoc documentation: Bio::PopGen::Statistics | CPAN documentation: Bio::PopGen::Statistics |
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Contents |
Introduction
This module and Bio::PopGen::PopStats provide implementation of several summary statistics for population genetics.
Supported statistics
- pi
- theta
- Tajima's D
- Fu and Li's D
- Fu and Li's D*
- Fu and Li's F
- Fu and Li's F*
- composite LD (for unphased haplotypes)
See also the supporting paper bibkey_perlymorphism2005 and those using Fst bibkey_rockman2003 and LD bibkey_hahnFIV from this and the other PopGen modules.
Known Bugs and Problems
As covered briefly in the Project priority list these computations can be slow - but the problem is not so much in the calculation code but in the creation and destruction of all the objects (Population, Individuals, and Genotype). In particular when doing simulations this can be very inefficient and we should provide a streamlined interface to the data so that the calculations can be sped up. There are methods in the Bio::PopGen::PopStats module for directly calculating the statistics and they end with _counts.
You may need to also convert populations to haploid state first before computing the statistics. This is achieved with the code:
my $happop = $pop->haploid_population
References
<biblio>
#bibkey_perlymorphism2005 pmid=15356276 </biblio>
<biblio>
#bibkey_rockman2003 pmid=14654003 </biblio>
<biblio>
#bibkey_hahnFIV pmid=15238535 </biblio>
