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Bio::PopGen::StatisticUser Contributed Perl DocumentBio::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	:

perl v5.24.1			  2017-07-08	    Bio::PopGen::Statistics(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich, Matthew Hahn | APPENDIX

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