Module:Bio::PopGen::Statistics

Bio::PopGen::Statistics
PDoc	Bio::PopGen::Statistics
CPAN	Bio::PopGen::Statistics
metaCPAN	Bio::PopGen::Statistics

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 [1] and those using Fst [2] and LD [3] 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

1. Stajich JE and Hahn MW. Disentangling the effects of demography and selection in human history. Mol Biol Evol. 2005 Jan;22(1):63-73. DOI:10.1093/molbev/msh252 |

2. Rockman MV, Hahn MW, Soranzo N, Goldstein DB, and Wray GA. Positive selection on a human-specific transcription factor binding site regulating IL4 expression. Curr Biol. 2003 Dec 2;13(23):2118-23.

3. Hahn MW, Rockman MV, Soranzo N, Goldstein DB, and Wray GA. Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the factor VII locus in humans. Genetics. 2004 Jun;167(2):867-77. DOI:10.1534/genetics.103.025726 |