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Manual Reference Pages  -  BIO::POPGEN::POPULATION (3)

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NAME

Bio::PopGen::Population - A population of individuals

CONTENTS

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 = $population->get_Marker($name);
  }

  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://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 _

    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



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