Bio::PopGen::Statistics(3)

NAME
Bio::PopGen::Statistics - Population Genetics statistical tests

SYNOPSIS
  use Bio::PopGen::Statistics;
  use Bio::AlignIO;
  use Bio::PopGen::IO;
  use Bio::PopGen::Simulation::Coalescent;

  my $sim = Bio::PopGen::Simulation::Coalescent->new( -sample_size => 12);

  my $tree = $sim->next_tree;

  $sim->add_Mutations($tree,20);

  my $stats = Bio::PopGen::Statistics->new();
  my $individuals = [ $tree->get_leaf_nodes];
  my $pi = $stats->pi($individuals);
  my $D  = $stats->tajima_D($individuals);

  # Alternatively to do this on input data from
  # See the tests in t/PopGen.t for more examples
  my $parser = Bio::PopGen::IO->new(-format => 'prettybase',
                                   -file   => 't/data/popstats.prettybase');
  my $pop = $parser->next_population;
  # Note that you can also call the stats as a class method if you like
  # the only reason to instantiate it (as above) is if you want
  # to set the verbosity for debugging
  $pi     = Bio::PopGen::Statistics->pi($pop);
  $theta  = Bio::PopGen::Statistics->theta($pop);

  # Pi and Theta also take additional arguments,
  # see the documentation for more information

  use Bio::PopGen::Utilities;
  use Bio::AlignIO;

  my $in = Bio::AlignIO->new(-file   => 't/data/t7.aln',
                            -format => 'clustalw');
  my $aln = $in->next_aln;
  # get a population, each sequence is an individual and
  # for the default case, every site which is not monomorphic
  # is a 'marker'.  Each individual will have a 'genotype' for the
  # site which will be the specific base in the alignment at that
  # site

  my $pop = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln);

DESCRIPTION
This object is intended to provide implementations some standard population genetics statistics about alleles in populations.

This module was previously named Bio::Tree::Statistics.

This object is a place to accumulate routines for calculating various statistics from the coalescent simulation, marker/allele, or from aligned sequence data given that you can calculate alleles, number of segregating sites.

Currently implemented:
 Fu and Li's D (fu_and_li_D)
 Fu and Li's D* (fu_and_li_D_star)
 Fu and Li's F (fu_and_li_F)
 Fu and Li's F* (fu_and_li_F_star)
 Tajima's D (tajima_D)
 Watterson's theta (theta)
 pi (pi) - number of pairwise differences
 composite_LD (composite_LD)
 McDonald-Kreitman (mcdonald_kreitman or MK)

Count based methods also exist in case you have already calculated the key statistics (seg sites, num individuals, etc) and just want to compute the statistic.

In all cases where a the method expects an arrayref of Bio::PopGen::IndividualI objects and Bio::PopGen::PopulationI object will also work.

  REFERENCES
Fu Y.X and Li W.H. (1993) "Statistical Tests of Neutrality of Mutations." Genetics 133:693-709.

Fu Y.X. (1996) "New Statistical Tests of Neutrality for DNA samples from a Population." Genetics 143:557-570.

McDonald J, Kreitman M.

Tajima F. (1989) "Statistical method for testing the neutral mutation hypothesis by DNA polymorphism." Genetics 123:585-595.

  CITING THIS WORK
Please see this reference for use of this implementation.

Stajich JE and Hahn MW "Disentangling the Effects of Demography and Selection in Human History." (2005) Mol Biol Evol 22(1):63-73.

If you use these Bio::PopGen modules please cite the Bioperl publication (see FAQ) and the above reference.

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  Support
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich, Matthew Hahn
Email jason-at-bioperl-dot-org Email matthew-dot-hahn-at-duke-dot-edu

McDonald-Kreitman implementation based on work by Alisha Holloway at UC Davis.

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  new
 Title   : new
 Usage   : my $obj = Bio::PopGen::Statistics->new();
 Function: Builds a new Bio::PopGen::Statistics object
 Returns : an instance of Bio::PopGen::Statistics
 Args    : none

  fu_and_li_D
 Title   : fu_and_li_D
 Usage   : my $D = $statistics->fu_and_li_D(\@ingroup,\@outgroup);
            OR
           my $D = $statistics->fu_and_li_D(\@ingroup,$extmutations);
 Function: Fu and Li D statistic for a list of individuals
           given an outgroup and the number of external mutations
           (either provided or calculated from list of outgroup individuals)
 Returns : decimal
 Args    : $individuals - array reference which contains ingroup individuals
           (L<Bio::PopGen::Individual> or derived classes)
           $extmutations - number of external mutations OR
           arrayref of outgroup individuals

  fu_and_li_D_counts
 Title   : fu_li_D_counts
 Usage   : my $D = $statistics->fu_and_li_D_counts($samps,$sites,
                                                   $external);
 Function: Fu and Li D statistic for the raw counts of the number
           of samples, sites, external and internal mutations
 Returns : decimal number
 Args    : number of samples (N)
           number of segregating sites (n)
           number of external mutations (n_e)

  fu_and_li_D_star
 Title   : fu_and_li_D_star
 Usage   : my $D = $statistics->fu_an_li_D_star(\@individuals);
 Function: Fu and Li's D* statistic for a set of samples
            Without an outgroup
 Returns : decimal number
 Args    : array ref of L<Bio::PopGen::IndividualI> objects
           OR
           L<Bio::PopGen::PopulationI> object

  fu_and_li_D_star_counts
 Title   : fu_li_D_star_counts
 Usage   : my $D = $statistics->fu_and_li_D_star_counts($samps,$sites,
                                                        $singletons);

 Function: Fu and Li D statistic for the raw counts of the number
           of samples, sites, external and internal mutations
 Returns : decimal number
 Args    : number of samples (N)
           number of segregating sites (n)
           singletons (n_s)

  fu_and_li_F
 Title   : fu_and_li_F
 Usage   : my $F = Bio::PopGen::Statistics->fu_and_li_F(\@ingroup,$ext_muts);
 Function: Calculate Fu and Li's F on an ingroup with either the set of
           outgroup individuals, or the number of external mutations
 Returns : decimal number
 Args    : array ref of L<Bio::PopGen::IndividualI> objects for the ingroup
           OR a L<Bio::PopGen::PopulationI> object
           number of external mutations OR list of individuals for the outgroup

  fu_and_li_F_counts
 Title   : fu_li_F_counts
 Usage   : my $F = $statistics->fu_and_li_F_counts($samps,$pi,
                                                   $sites,
                                                   $external);
 Function: Fu and Li F statistic for the raw counts of the number
           of samples, sites, external and internal mutations
 Returns : decimal number
 Args    : number of samples (N)
           average pairwise differences (pi)
           number of segregating sites (n)
           external mutations (n_e)

  fu_and_li_F_star
 Title   : fu_and_li_F_star
 Usage   : my $F = Bio::PopGen::Statistics->fu_and_li_F_star(\@ingroup);
 Function: Calculate Fu and Li's F* on an ingroup without an outgroup
           It uses count of singleton alleles instead
 Returns : decimal number
 Args    : array ref of L<Bio::PopGen::IndividualI> objects for the ingroup
           OR
           L<Bio::PopGen::PopulationI> object

  fu_and_li_F_star_counts
 Title   : fu_li_F_star_counts
 Usage   : my $F = $statistics->fu_and_li_F_star_counts($samps,
                                                   $pi,$sites,
                                                   $singletons);
 Function: Fu and Li F statistic for the raw counts of the number
           of samples, sites, external and internal mutations
 Returns : decimal number
 Args    : number of samples (N)
           average pairwise differences (pi)
           number of segregating sites (n)
           singleton  mutations (n_s)

  tajima_D
 Title   : tajima_D
 Usage   : my $D = Bio::PopGen::Statistics->tajima_D(\@samples);
 Function: Calculate Tajima's D on a set of samples
 Returns : decimal number
 Args    : array ref of L<Bio::PopGen::IndividualI> objects
           OR
           L<Bio::PopGen::PopulationI> object

  tajima_D_counts
 Title   : tajima_D_counts
 Usage   : my $D = $statistics->tajima_D_counts($samps,$sites,$pi);
 Function: Tajima's D statistic for the raw counts of the number
           of samples, sites, and avg pairwise distances (pi)
 Returns : decimal number
 Args    : number of samples (N)
           number of segregating sites (n)
           average pairwise differences (pi)

  pi
 Title   : pi
 Usage   : my $pi = Bio::PopGen::Statistics->pi(\@inds)
 Function: Calculate pi (average number of pairwise differences) given
           a list of individuals which have the same number of markers
           (also called sites) as available from the get_Genotypes()
           call in L<Bio::PopGen::IndividualI>
 Returns : decimal number
 Args    : Arg1= array ref of L<Bio::PopGen::IndividualI> objects
             which have markers/mutations.  We expect all individuals to
             have a marker - we will deal with missing data as a special case.
           OR
           Arg1= L<Bio::PopGen::PopulationI> object.  In the event that
                 only allele frequency data is available, storing it in
                 Population object will make this available.
           num sites [optional], an optional second argument (integer)
             which is the number of sites, then pi returned is pi/site.

  theta
 Title   : theta
 Usage   : my $theta = Bio::PopGen::Statistics->theta($sampsize,$segsites);
 Function: Calculates Watterson's theta from the sample size
           and the number of segregating sites.
           Providing the third parameter, total number of sites will
           return theta per site.
           This is also known as K-hat = K / a_n
 Returns : decimal number
 Args    : sample size (integer),
           num segregating sites (integer)
           total sites (integer) [optional] (to calculate theta per site)
           OR
           provide an arrayref of the L<Bio::PopGen::IndividualI> objects
           total sites (integer) [optional] (to calculate theta per site)
           OR
           provide an L<Bio::PopGen::PopulationI> object
           total sites (integer)[optional]

  singleton_count
 Title   : singleton_count
 Usage   : my ($singletons) = Bio::PopGen::Statistics->singleton_count(\@inds)
 Function: Calculate the number of mutations/alleles which only occur once in
           a list of individuals for all sites/markers
 Returns : (integer) number of alleles which only occur once (integer)
 Args    : arrayref of L<Bio::PopGen::IndividualI> objects
           OR
           L<Bio::PopGen::PopulationI> object

  segregating_sites_count
 Title   : segregating_sites_count
 Usage   : my $segsites = Bio::PopGen::Statistics->segregating_sites_count
 Function: Gets the number of segregating sites (number of polymorphic sites)
 Returns : (integer) number of segregating sites
 Args    : arrayref of L<Bio::PopGen::IndividualI> objects
           OR
           L<Bio::PopGen::PopulationI> object

  heterozygosity
 Title   : heterozygosity
 Usage   : my $het = Bio::PopGen::Statistics->heterozygosity($sampsize,$freq1);
 Function: Calculate the heterozgosity for a sample set for a set of alleles
 Returns : decimal number
 Args    : sample size (integer)
           frequency of one allele (fraction - must be less than 1)
           [optional] frequency of another allele - this is only needed
                      in a non-binary allele system

Note : p^2 + 2pq + q^2

  derived_mutations
 Title   : derived_mutations
 Usage   : my $ext = Bio::PopGen::Statistics->derived_mutations($ingroup,$outgroup);
 Function: Calculate the number of alleles or (mutations) which are ancestral
           and the number which are derived (occurred only on the tips)
 Returns : array of 2 items - number of external and internal derived
           mutation
 Args    : ingroup - L<Bio::PopGen::IndividualI>s arrayref OR
                     L<Bio::PopGen::PopulationI>
           outgroup- L<Bio::PopGen::IndividualI>s arrayref OR
                     L<Bio::PopGen::PopulationI> OR
                     a single L<Bio::PopGen::IndividualI>

  composite_LD
 Title   : composite_LD
 Usage   : %matrix = Bio::PopGen::Statistics->composite_LD($population);
 Function: Calculate the Linkage Disequilibrium
           This is for calculating LD for unphased data.
           Other methods will be appropriate for phased haplotype data.

 Returns : Hash of Hashes - first key is site 1,second key is site 2
           and value is LD for those two sites.
           my $LDarrayref = $matrix{$site1}->{$site2};
           my ($ldval, $chisquared) = @$LDarrayref;
 Args    : L<Bio::PopGen::PopulationI> or arrayref of
           L<Bio::PopGen::IndividualI>s
 Reference: Weir B.S. (1996) "Genetic Data Analysis II",
                      Sinauer, Sunderlanm MA.

  mcdonald_kreitman
 Title   : mcdonald_kreitman
 Usage   : $Fstat = mcdonald_kreitman($ingroup, $outgroup);
 Function: Calculates McDonald-Kreitman statistic based on a set of ingroup
           individuals and an outgroup by computing the number of
           differences at synonymous and non-synonymous sites
           for intraspecific comparisons and with the outgroup
 Returns : 2x2 table, followed by a hash reference indicating any
           warning messages about the status of the alleles or codons
 Args    : -ingroup    => L<Bio::PopGen::Population> object or
                          arrayref of L<Bio::PopGen::Individual>s
           -outgroup   => L<Bio::PopGen::Population> object or
                          arrayef of L<Bio::PopGen::Individual>s
           -polarized  => Boolean, to indicate if this should be
                          a polarized test. Must provide two individuals
                          as outgroups.

  mcdonald_kreitman_counts
 Title   : mcdonald_kreitman_counts
 Usage   : my $MK = $statistics->mcdonald_kreitman_counts(

             N_poly -> integer of count of non-syn polymorphism
             N_fix  -> integer of count of non-syn fixed substitutions
             S_poly -> integer of count of syn polymorphism
             S_fix  -> integer of count of syn fixed substitutions
                                                          );
 Function:
 Returns : decimal number
 Args    :