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Man Pages


Manual Reference Pages  -  BIO::POPGEN::INDIVIDUALI (3)

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NAME

Bio::PopGen::IndividualI - An individual who has Genotype or Sequence Results

CONTENTS

SYNOPSIS



  # Get a Bio::PopGen::IndividualI somehow
  # test if it has alleles/genotypes for a given marker
  if( $ind->has_marker($markername) ) {
  }
  # get the unique id
  print $ind->unique_id, "\n";

  # get the number of results (genotypes)
  print $ind->num_results;



DESCRIPTION

Describe the interface here

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://github.com/bioperl/bioperl-live/issues



AUTHOR - Jason Stajich

Email jason-at-bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

    unique_id



 Title   : unique_id
 Usage   : my $id = $individual->unique_id
 Function: Unique Identifier
 Returns : string representing unique identifier
 Args    : string



    num_genotypes



 Title   : num_genotypes
 Usage   : my $count = $person->num_results;
 Function: returns the count of the number of Results for a person
 Returns : integer
 Args    : none



    annotation



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



    get_Genotypes



 Title   : get_Genotypes
 Usage   : my @genotypes = $ind->get_Genotypes(-marker => $markername);
 Function: Get the genotypes for an individual, based on a criteria
 Returns : Array of genotypes
 Args    : either none (return all genotypes) or
           -marker => name of marker to return (exact match, case matters)



    has_Marker



 Title   : has_Marker
 Usage   : if( $ind->has_Marker($name) ) {}
 Function: Boolean test to see if an Individual has a genotype
           for a specific marker
 Returns : Boolean (true or false)
 Args    : String representing a marker name



    get_marker_names



 Title   : get_marker_names
 Usage   : my @names = $individual->get_marker_names;
 Function: Returns the list of known marker names
 Returns : List of strings
 Args    : none



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perl v5.20.3 BIO::POPGEN::INDIVIDUALI (3) 2016-04-05

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