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Bio::PopGen::MarkerI.3pm

NAME

Bio::PopGen::MarkerI - A Population Genetic conceptual marker

SYNOPSIS

# 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
 
 

DESCRIPTION

This is the basic interface for Markers which one can associate alleles with for calculating Theta and Pi.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

CONTRIBUTORS

Matthew Hahn, matthew.hahn-at-duke.edu

APPENDIX

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