Bio::PopGen PopulationI
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Summary
Bio::PopGen::PopulationI - Interface for Populations
Package variables
No package variables defined.
Included modules
Carp
Inherit
Bio::Root::RootI
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.
Methods
nameDescriptionCode
descriptionDescriptionCode
sourceDescriptionCode
annotationDescriptionCode
get_IndividualsDescriptionCode
get_GenotypesDescriptionCode
get_MarkerDescriptionCode
get_marker_namesDescriptionCode
get_MarkersDescriptionCode
get_number_individualsDescriptionCode
Methods description
namecode    nextTop
 Title   : name
Usage : my $name = $pop->name
Function: Get the population name
Returns : string representing population name
Args : [optional] string representing population name
descriptioncodeprevnextTop
 Title   : description
Usage : my $description = $pop->description
Function: Get the population description
Returns : string representing population description
Args : [optional] string representing population description
sourcecodeprevnextTop
 Title   : source
Usage : my $source = $pop->source
Function: Get the population source
Returns : string representing population source
Args : [optional] string representing population source
annotationcodeprevnextTop
 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_IndividualscodeprevnextTop
 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
get_GenotypescodeprevnextTop
 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
get_MarkercodeprevnextTop
 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
get_marker_namescodeprevnextTop
 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_MarkerscodeprevnextTop
 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_individualscodeprevnextTop
 Title   : get_number_individuals
Usage : my $count = $pop->get_number_individuals;
Function: Get the count of the number of individuals
Returns : integer >= 0
Args : [optional] marker name, will return a count of the number
of individuals which have this marker
Methods code
namedescriptionprevnextTop
sub name {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
descriptiondescriptionprevnextTop
sub description {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
sourcedescriptionprevnextTop
sub source {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
annotationdescriptionprevnextTop
sub annotation {
   my ($self) = @_;
   $self->throw_not_implemented();
}
get_IndividualsdescriptionprevnextTop
sub get_Individuals {
    shift->throw_not_implemented();
}
get_GenotypesdescriptionprevnextTop
sub get_Genotypes {
    shift->throw_not_implemented;
}
get_MarkerdescriptionprevnextTop
sub get_Marker {
    shift->throw_not_implemented();
}
get_marker_namesdescriptionprevnextTop
sub get_marker_names {
    my ($self) = @_;
    $self->throw_not_implemented();
}
get_MarkersdescriptionprevnextTop
sub get_Markers {
    my ($self) = shift;
    return map { $self->get_Marker($_) } $self->get_marker_names();
}
get_number_individualsdescriptionprevnextTop
sub get_number_individuals {
   my ($self) = @_;
   $self->throw_not_implemented();
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 StajichTop
Email jason-at-bioperl.org
CONTRIBUTORSTop
Matthew Hahn, matthew.hahn-at-duke.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _