Bio::PopGen::PopulationI - Interface for Populations # 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"; } 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.

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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 _

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

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

number_individuals
Title : number_individuals Usage : my $count = $pop->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