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://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::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
marker_coverage¶
Title : marker_coverage
Usage : $marker->marker_coverage();
Function: Get marker coverage, that is, the number of
individuals where the marker is present
excluding missing or ambiguous alleles
Returns : integer, representing marker coverage
Args :