| Bio::PopGen::Population(3pm) | User Contributed Perl Documentation | Bio::PopGen::Population(3pm) |
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');
$population->add_Individual($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;
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.
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
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.
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
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 _
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
OR
-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 relevant 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
| 2018-10-27 | perl v5.26.2 |