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Bio::PopGen::Individual.3pm

NAME

Bio::PopGen::Individual - An implementation of an Individual who has Genotype or Sequence Results

SYNOPSIS

   use Bio::PopGen::Individual;
 
   my $ind = Bio::PopGen::Individual->new(-unique_id => $id,
                                         -genotypes => \@genotypes);
 
 

DESCRIPTION

This object is a container for genotypes.

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:

   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 _

new

  Title   : new
  Usage   : my $obj = Bio::PopGen::Individual->new();
  Function: Builds a new Bio::PopGen::Individual object 
  Returns : an instance of Bio::PopGen::Individual
  Args    : -unique_id => $id,
            -genotypes => \@genotypes
 
 

unique_id

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

num_of_results

  Title   : num_of_results
  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
 
 

add_Genotype

  Title   : add_Genotype
  Usage   : $individual->add_Genotype
  Function: add a genotype value
  Returns : count of the number of genotypes associated with this individual
  Args    : @genotypes - L<Bio::PopGen::GenotypeI> object(s) containing 
                         alleles plus a marker name
 
 

reset_Genotypes

  Title   : reset_Genotypes
  Usage   : $individual->reset_Genotypes;
  Function: Reset the genotypes stored for this individual
  Returns : none
  Args    : none
 
 

remove_Genotype

  Title   : remove_Genotype
  Usage   : $individual->remove_Genotype(@names)
  Function: Removes the genotypes for the requested markers
  Returns : none
  Args    : Names of markers
 
 

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