Bio::PopGen::Individual(3pm) User Contributed Perl Documentation 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:
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::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
perl v5.14.2 2012-03-02 Bio::PopGen::Individual(3pm)