Bio::PopGen::PopulationI(3)

NAME
Bio::PopGen::PopulationI - Interface for Populations

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

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

  print "For marker $markername:\n";
  foreach my $genotype ( $population->get_Genotypes(-marker => $markername) ) {
      print "Individual ", $genotype->individual_id, " genotype alleles are ",
      join(',', $genotype->get_Alleles()), "\n";
  }
  # 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}\n";
  }

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://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 _

  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