Bio::PopGen::MarkerI(3) 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,


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : name
 Usage   : my $name = $marker->name();
 Function: Get the name of the marker
 Returns : string representing the name of the marker
 Args    :


 Title   : description
 Usage   : my $desc = $marker->description
 Function: Get the marker description free text
 Returns : string
 Args    : [optional] string


 Title   : type
 Usage   : my $type = $marker->type;
 Function: Get coded string for marker type
 Returns : string
 Args    : [optional] string


 Title   : unique_id
 Usage   : my $id = $marker->unique_id;
 Function: Get the unique marker ID
 Returns : unique ID string
 Args    : [optional ] string


 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.


 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


 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