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

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:

	 https://redmine.open-bio.org/projects/bioperl/

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

perl v5.14.2							    2012-03-02					      Bio::PopGen::Population(3pm)