Reference

Bio::PopGen::Individual(3pm)

An implementation of an Individual who has Genotype or Sequence Results

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

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

History