Bio::PopGen::PopulationI(3pm) User Contributed Perl Documentation Bio::PopGen::PopulationI(3pm)
NAME
Bio::PopGen::PopulationI - Interface for Populations
SYNOPSIS
# Get Bio::PopGen::PopulationI object somehow, like
# from Bio::Population::Population
print "name is ", $population->name(), "
";
print "source is ", $population->source(), "
";
print "description is ", $population->description(), "
";
print "For marker $markername:
";
foreach my $genotype ( $population->get_Genotypes(-marker => $markername) ) {
print "Individual ", $genotype->individual_id, " genotype alleles are ",
join(',', $genotype->get_Alleles()), "
";
}
# 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}
";
}
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
perl v5.14.2 2012-03-02 Bio::PopGen::PopulationI(3pm)