Bio::PopGen::Marker(3pm) User Contributed Perl Documentation Bio::PopGen::Marker(3pm)
NAME
Bio::PopGen::Marker - A genetic marker which one uses to generate genotypes
SYNOPSIS
my $name = $marker->name(); # marker name
my $description = $marker->description(); # description
my $type = $marker->type(); # coded type of the marker
my $unique_id = $marker->unique_id; # optional unique ID
my @alleles = $marker->get_Alleles(); # the known alleles
my %allele_freqs = $marker->get_Allele_Frequencies(); # keys are marker names
# vals are frequencies
# may change to handle multiple populations
DESCRIPTION
This object will not contain genotype information pertaining to an individual, but rather population level statistics and descriptive
information about a marker.
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::Marker->new();
Function: Builds a new Bio::PopGen::Marker object
Returns : an instance of Bio::PopGen::Marker
Args : -name => [string] marker name
-description => [string] marker description
-type => [string] marker type
-unique_id => [string/int] unique id
-allele_freq => [hash ref] allele frequencies
name
Title : name
Usage : my $name = $marker->name();
Function: Get the name of the marker
Returns : string representing the name of the marker
Args : [optional] name
description
Title : description
Usage : my $desc = $marker->description
Function: Get the marker description free text
Returns : string
Args : [optional] string
type
Title : type
Usage : my $type = $marker->type;
Function: Get coded string for marker type
Returns : string
Args : [optional] string
unique_id
Title : unique_id
Usage : my $id = $marker->unique_id;
Function: Get the unique marker ID
Returns : unique ID string
Args : [optional ] string
annotation
Title : annotation
Usage : my $annotation_collection = $marker->annotation;
Function: Get/set a Bio::AnnotationCollectionI for this marker
Returns : Bio::AnnotationCollectionI object
Args : [optional set] Bio::AnnotationCollectionI object
get_Alleles
Title : get_Alleles
Usage : my @alleles = $marker->get_Alleles();
Function: Get the available marker alleles
Returns : Array of strings
Args : none
get_Allele_Frequencies
Title : get_Allele_Frequencies
Usage : my %allele_freqs = $marker->get_Allele_Frequencies;
Function: Get the alleles and their frequency (set relative to
a given population - you may want to create different
markers with the same name for different populations
with this current implementation
Returns : Associative array where keys are the names of the alleles
Args : none
add_Allele_Frequency
Title : add_Allele_Frequency
Usage : $marker->add_Allele_Frequency($allele,$freq)
Function: Adds an allele frequency
Returns : None
Args : $allele - allele name
$freq - frequency value
reset_alleles
Title : reset_alleles
Usage : $marker->reset_alleles();
Function: Reset the alleles for a marker
Returns : None
Args : None
perl v5.14.2 2012-03-02 Bio::PopGen::Marker(3pm)