Module:Bio::PopGen::Statistics

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


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 [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

Error fetching PMID 15356276:
  1. Error fetching PMID 15356276: [bibkey_perlymorphism2005]
Error fetching PMID 14654003:
  1. Error fetching PMID 14654003: [bibkey_rockman2003]
Error fetching PMID 15238535:
  1. Error fetching PMID 15238535: [bibkey_hahnFIV]
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