Christopher Fields > BioPerl > Bio::PopGen::Population



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Module Version: 1.006924   Source  


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


  use Bio::PopGen::Population;
  use Bio::PopGen::Individual;
  my $population = Bio::PopGen::Population->new();
  my $ind = Bio::PopGen::Individual->new(-unique_id => 'id');

  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;


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.


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AUTHOR - Jason Stajich ^



Matthew Hahn,


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 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)


 Title   : name
 Usage   : my $name = $pop->name
 Function: Get the population name
 Returns : string representing population name
 Args    : [optional] string representing population name


 Title   : description
 Usage   : my $description = $pop->description
 Function: Get the population description
 Returns : string representing population description
 Args    : [optional] string representing population description


 Title   : source
 Usage   : my $source = $pop->source
 Function: Get the population source
 Returns : string representing population source
 Args    : [optional] string representing population source


 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


 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
           -frequencies => { 'marker1' => { 'allele1' => 0.01,
                                            'allele2' => 0.99},
                             'marker2' => ...


 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


 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


 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


 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


 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


 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


 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


 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.


 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


 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


 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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