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