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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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-eduMcDonald-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 :