NAME¶
Bio::PopGen::PopulationI - Interface for Populations
SYNOPSIS¶
# 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";
}
DESCRIPTION¶
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.
FEEDBACK¶
Mailing Lists¶
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
Support¶
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.
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:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich¶
Email jason-at-bioperl.org
CONTRIBUTORS¶
Matthew Hahn, matthew.hahn-at-duke.edu
APPENDIX¶
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
annotation¶
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
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
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 : [optional] marker name, will return a count of the number
of individuals which have this marker