| Bio::PopGen::PopulationI(3pm) | User Contributed Perl Documentation | Bio::PopGen::PopulationI(3pm) |
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.
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.
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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:
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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 : 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 : 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
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
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
Title : get_marker_names Usage : my @names = $pop->get_marker_names; Function: Get the names of the markers Returns : Array of strings Args : none
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
Title : get_number_individuals
Usage : my $count = $pop->get_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
| 2018-10-27 | perl v5.26.2 |