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bio::popgen::statistics(3pm) [debian man page]

Bio::PopGen::Statistics(3pm)				User Contributed Perl Documentation			      Bio::PopGen::Statistics(3pm)

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://redmine.open-bio.org/projects/bioperl/ 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 v5.14.2 2012-03-02 Bio::PopGen::Statistics(3pm)
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