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Bio::PopGen::Marker(3)User Contributed Perl DocumentatioBio::PopGen::Marker(3)

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	:

perl v5.24.1			  2017-07-08		Bio::PopGen::Marker(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | CONTRIBUTORS | APPENDIX

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