Bio::PopGen::Statistics.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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    :