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

NAME

       Bio::PopGen::PopulationI - Interface for Populations

SYNOPSIS

	 # Get Bio::PopGen::PopulationI object somehow, like
	 # from Bio::Population::Population

	 print "name is ", $population->name(), "
";
	 print "source is ", $population->source(), "
";
	 print "description is ", $population->description(), "
";

	 print "For marker $markername:
";
	 foreach my $genotype ( $population->get_Genotypes(-marker => $markername) ) {
	     print "Individual ", $genotype->individual_id, " genotype alleles are ",
	     join(',', $genotype->get_Alleles()), "
";
	 }
	 # get a marker with allele frequencies calculated from the population
	 my $marker = $population->get_Marker($markername);
	 my %af = $marker->get_Allele_Frequencies;
	 foreach my $allele ( keys %af ) {
	     print "$allele $af{$allele}
";
	 }

DESCRIPTION

       This interface describes the basics of a population.  One can use this object to get the genotypes of specific individuals, only those
       individuals which have a certain marker, or create a marker with allele frequency information.

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 _

   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

   get_Individuals
	Title	: get_Individuals
	Usage	: my @inds = $pop->get_Individuals();
	Function: Return the individuals, alternatively restrict by a criteria
	Returns : Array of L<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 L<Bio::PopGen::GenotypeI> objects
	Args	: -marker => name of the marker

   get_Marker
	Title	: get_Marker
	Usage	: my $marker = $population->get_Marker($name)
	Function: Get a Bio::PopGen::Marker object based on this population
	Returns : L<Bio::PopGen::MarkerI> object
	Args	: 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	: none

   get_Markers
	Title	: get_Markers
	Usage	: my @markers = $pop->get_Markers();
	Function: Will retrieve a list of instantiated MarkerI objects
		  for a population.  This is a convience method combining
		  get_marker_names with get_Marker
	Returns : List of array of Bio::PopGen::MarkerI objects
	Args	: none

   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	: [optional] marker name, will return a count of the number
		  of individuals which have this marker

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