Bio::PopGen::Population.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::PopGen::Population - A population of individuals

SYNOPSIS

   use Bio::PopGen::Population;
   use Bio::PopGen::Individual;
   my $population = Bio::PopGen::Population->new();
   my $ind = Bio::PopGen::Individual->new(-unique_id => 'id');
   $population->add_Individual($ind);
 
   for my $ind ( $population->get_Individuals ) {
     # iterate through the individuals
   }
 
   for my $name ( $population->get_marker_names ) {
     my $marker = $population->get_Marker();
   }
 
   my $num_inds = $population->get_number_individuals;
 
   my $homozygote_f   = $population->get_Frequency_Homozygotes;
   my $heterozygote_f = $population->get_Frequency_Heterozygotes;
 
   # make a population haploid by making fake chromosomes through
   # haplotypes -- ala allele 1 is on chrom 1 and allele 2 is on chrom 2 
   # the number of individuals created will thus be 2 x number in
   # population
   my $happop = $population->haploid_population;
 
 

DESCRIPTION

This is a collection of individuals. We'll have ways of generating Bio::PopGen::MarkerI objects out so we can calculate allele_frequencies for implementing the various statistical tests.

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 email or the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

CONTRIBUTORS

Matthew Hahn, matthew.hahn-at-duke.edu

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::Population->new();
  Function: Builds a new Bio::PopGen::Population object 
  Returns : an instance of Bio::PopGen::Population
  Args    : -individuals => array ref of individuals (optional)
            -name        => population name (optional)
            -source      => a source tag (optional)
            -description => a short description string of the population (optional)
 
 

name

  Title   : name
  Usage   : my $name = $pop->name
  Function: Get the population name
  Returns : string representing population name
  Args    : [optional] string representing population name
 
 

description

  Title   : description
  Usage   : my $description = $pop->description
  Function: Get the population description
  Returns : string representing population description
  Args    : [optional] string representing population description
 
 

source

  Title   : source
  Usage   : my $source = $pop->source
  Function: Get the population source
  Returns : string representing population source
  Args    : [optional] string representing population source
 
 

annotation

  Title   : annotation
  Usage   : my $annotation_collection = $pop->annotation;
  Function: Get/set a Bio::AnnotationCollectionI for this population
  Returns : Bio::AnnotationCollectionI object
  Args    : [optional set] Bio::AnnotationCollectionI object
 
 

set_Allele_Frequency

  Title   : set_Allele_Frequency
  Usage   : $population->set_Allele_Frequency('marker' => { 'allele1' => 0.1});
  Function: Sets an allele frequency for a Marker for this Population
            This allows the Population to not have individual individual
            genotypes but rather a set of overall allele frequencies
  Returns : Count of the number of markers
  Args    : -name      => (string) marker name
            -allele    => (string) allele name
            -frequency => (double) allele frequency - must be between 0 and 1
            OR
            -frequencies => { 'marker1' => { 'allele1' => 0.01,
                                             'allele2' => 0.99},
                              'marker2' => ...
                             }
 
 

add_Individual

  Title   : add_Individual
  Usage   : $population->add_Individual(@individuals);
  Function: Add individuals to a population
  Returns : count of the current number in the object 
  Args    : Array of Individuals
 
 

remove_Individuals

  Title   : remove_Individuals
  Usage   : $population->remove_Individuals(@ids);
  Function: Remove individual(s) to a population
  Returns : count of the current number in the object 
  Args    : Array of ids
 
 

get_Individuals

  Title   : get_Individuals
  Usage   : my @inds = $pop->get_Individuals();
  Function: Return the individuals, alternatively restrict by a criteria
  Returns : Array of Bio::PopGen::IndividualI objects
  Args    : none if want all the individuals OR,
            -unique_id => To get an individual with a specific id
            -marker    => To only get individuals which have a genotype specific
                         for a specific marker name
 
 

get_Genotypes

  Title   : get_Genotypes
  Usage   : my @genotypes = $pop->get_Genotypes(-marker => $name)
  Function: Get the genotypes for all the individuals for a specific
            marker name
  Returns : Array of Bio::PopGen::GenotypeI objects
  Args    : -marker => name of the marker
 
 

get_marker_names

  Title   : get_marker_names
  Usage   : my @names = $pop->get_marker_names;
  Function: Get the names of the markers
  Returns : Array of strings
  Args    : [optional] boolean flag to ignore internal cache status
 
 

get_Marker

  Title   : get_Marker
  Usage   : my $marker = $population->get_Marker($name)
  Function: Get a Bio::PopGen::Marker object based on this population
  Returns : Bio::PopGen::MarkerI object
  Args    : name of the marker
 
 

get_number_individuals

  Title   : get_number_individuals
  Usage   : my $count = $pop->get_number_individuals;
  Function: Get the count of the number of individuals
  Returns : integer >= 0
  Args    : none
 
 

set_number_individuals

  Title   : set_number_individuals
     Usage   : $pop->set_number_individuals($num);
  Function: Fixes the number of individuals, call this with
            0 to unset.
            Only use this if you know what you are doing,
            this is only relavent when you are just adding
            allele frequency data for a population and want to
            calculate something like theta
  Returns : none
  Args    : individual count, calling it with undef or 0
             will reset the value to return a number
             calculated from the number of individuals
             stored for this population.
 
 

get_Frequency_Homozygotes

  Title   : get_Frequency_Homozygotes
  Usage   : my $freq = $pop->get_Frequency_Homozygotes;
  Function: Calculate the frequency of homozygotes in the population
  Returns : fraction between 0 and 1
  Args    : $markername
 
 

get_Frequency_Heterozygotes

  Title   : get_Frequency_Heterozygotes
  Usage   : my $freq = $pop->get_Frequency_Homozygotes;
  Function: Calculate the frequency of homozygotes in the population
  Returns : fraction between 0 and 1
  Args    : $markername
 
 

haploid_population

  Title   : haploid_population
  Usage   : my $pop = $population->haploid_population;
  Function: Make a new population where all the individuals
            are haploid - effectively an individual out of each
            chromosome an individual has.  
  Returns : L<Bio::PopGen::PopulationI>
  Args    : None