Christopher Fields > BioPerl-1.6.920 > Bio::PopGen::Marker

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Module Version: 1.006920   Source   Latest Release: BioPerl-1.6.924

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

marker_coverage

 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    : 
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