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BioPerl-1.6.920
River stage two • 60 direct dependents • 65 total dependents
/ Bio::PopGen::MarkerI

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:

https://redmine.open-bio.org/projects/bioperl/

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