Bio::PopGen::PopulationI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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