NAME

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

SYNOPSIS

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

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 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 _

new

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 

name

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

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

get_Alleles

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

add_Allele_Frequency

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

reset_alleles

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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq