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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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: http://bugzilla.bioperl.org/ 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 _

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