Provided by: libbio-perl-perl_1.7.2-2_all
Bio::PopGen::MarkerI - A Population Genetic conceptual marker
# Get a Bio::PopGen::MarkerI somehow - like using a Bio::PopGen::Marker my $name = $marker->name(); # marker name my $description = $marker->description(); # description my $type = $marker->type(); # coded type of the marker my $unique_id = $marker->unique_id; # optional unique ID my @alleles = $marker->get_Alleles(); # the known alleles my %allele_freqs = $marker->get_Allele_Frequencies(); # keys are marker names # vals are frequencies # may change to handle multiple populations
This is the basic interface for Markers which one can associate alleles with for calculating Theta and Pi.
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AUTHOR - Jason Stajich
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 _ name Title : name Usage : my $name = $marker->name(); Function: Get the name of the marker Returns : string representing the name of the marker Args : description Title : description Usage : my $desc = $marker->description Function: Get the marker description free text Returns : string Args : [optional] string type Title : type Usage : my $type = $marker->type; Function: Get coded string for marker type Returns : string Args : [optional] string unique_id Title : unique_id Usage : my $id = $marker->unique_id; Function: Get the unique marker ID Returns : unique ID string Args : [optional ] string annotation Title : annotation Usage : $obj->annotation($seq_obj) Function: retrieve the attached annotation object Returns : Bio::AnnotationCollectionI or none; See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information. This method comes through extension from Bio::AnnotatableI. get_Alleles Title : get_Alleles Usage : my @alleles = $marker->get_Alleles(); Function: Get the available marker alleles if they are known and stored Returns : Array of strings Args : none get_Allele_Frequencies Title : get_Allele_Frequencies Usage : my %allele_freqs = $marker->get_Allele_Frequencies; Function: Get the alleles and their frequency (set relative to a given population - you may want to create different markers with the same name for different populations with this current implementation Returns : Associative array (hash) where keys are the names of the alleles Args : none