Reference

Bio::PopGen::PopulationI(3pm)

Interface for Populations

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

History