Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::PopGen::Marker - A genetic marker which one uses to generate genotypes


         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 object will not contain genotype information pertaining to an individual, but rather
       population level statistics and descriptive information about a marker.


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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   : new
        Usage   : my $obj = Bio::PopGen::Marker->new();
        Function: Builds a new Bio::PopGen::Marker object
        Returns : an instance of Bio::PopGen::Marker
        Args    : -name          => [string] marker name
                  -description   => [string] marker description
                  -type          => [string] marker type
                  -unique_id     => [string/int] unique id
                  -allele_freq   => [hash ref] allele frequencies

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

        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   : my $annotation_collection = $marker->annotation;
        Function: Get/set a Bio::AnnotationCollectionI for this marker
        Returns : Bio::AnnotationCollectionI object
        Args    : [optional set] Bio::AnnotationCollectionI object

        Title   : get_Alleles
        Usage   : my @alleles = $marker->get_Alleles();
        Function: Get the available marker alleles
        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 where keys are the names of the alleles
        Args    : none

        Title   : add_Allele_Frequency
        Usage   : $marker->add_Allele_Frequency($allele,$freq)
        Function: Adds an allele frequency
        Returns : None
        Args    : $allele - allele name
                  $freq   - frequency value

        Title   : reset_alleles
        Usage   : $marker->reset_alleles();
        Function: Reset the alleles for a marker
        Returns : None
        Args    : None

        Title   : marker_coverage
        Usage   : $marker->marker_coverage();
        Function: Get marker coverage, that is, the number of
                  individuals where the marker is present
                  excluding missing or ambiguous alleles
        Returns : integer, representing marker coverage
        Args    :