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Bio::PopGen::Marker(3pm) User Contributed Perl Documentation Bio::PopGen::Marker(3pm)


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    :
2018-10-27 perl v5.26.2