/ 
BioPerl-1.007000_004
River stage two • 60 direct dependents • 65 total dependents
/ Bio::PopGen::Population

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 = $population->get_Marker($name);
}

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:

https://github.com/bioperl/bioperl-live/issues

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