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