Bio::PopGen::Population - A population of individuals Give standard usage here This is a collection of individuals. We'll have ways of generating Bio::PopGen::Marker objects out so we can calculate allele_frequencies for implementing the various statistical tests.

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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.bioperl.org/ Email jason-at-bioperl.org Matthew Hahn, matthew.hahn-at-duke.edu The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::PopGen::Population(); 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

set_Allele_Frequency
Title : set_Allele_Frequency Usage : $population->set_Allele_Frequency( 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