Bio::Map::LinkageMap(3pm)				User Contributed Perl Documentation				 Bio::Map::LinkageMap(3pm)

NAME

       Bio::Map::LinkageMap - A representation of a genetic linkage map.

SYNOPSIS

	   use Bio::Map::LinkageMap;
	       # create a new map
	   my $map = Bio::Map::LinkageMap->new(-name => 'Chads Superterriffic Map',
					     -type => 'Linkage',
					     -units=> 'cM');
	       # create the location of a marker for that map
	   my $position = Bio::Map::LinkagePosition->new( -positions => 1,
		       -distance => "22.3");
	       # create a marker and place it at that position
	   my $marker = Bio::Map::Marker::Microsatellite->new(
			       -name => 'SuuuperMarker',
			       -position => $position);
	       # place that marker on that map
	   $map->add_element($marker);

	       # done!

DESCRIPTION

       This object describes the basic functionality of a genetic linkage map in Bioperl. Each 'position' can have one or more markers that map
       some number of units from the markers at the previous position.

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 - Chad Matsalla
       Email bioinformatics1@dieselwurks.com

CONTRIBUTORS

       Lincoln Stein	   lstein@cshl.org Heikki Lehvaslaiho  heikki-at-bioperl-dot-org Jason Stajich	     jason@bioperl.org Sendu Bala
       bix@sendu.me.uk

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $linkage_map = Bio::Map::LinkageMap->new();
	Function: Builds a new Bio::Map::LinkageMap object
	Returns : Bio::Map::LinkageMap
	Args	: -name    => the name of the map (string) [optional]
		      -type    => the type of this map (string, defaults to Linkage) [optional]
		  -species => species for this map (Bio::Species) [optional]
		  -units   => the map units (string, defaults to cM) [optional]
		  -elements=> elements to initialize with
			      (arrayref of Bio::Map::MappableI objects) [optional]
		  -uid	    => Unique ID of this map

   length
	Title	: length
	Usage	: my $length = $map->length();
	Function: Retrieves the length of the map. In the case of a LinkageMap, the
		      length is the sum of all marker distances.
	Returns : An integer representing the length of this LinkageMap. Will return
		      0 if length is not calculateable
	Args	: None.

   add_element($marker)
	Title	: add_element($marker)
	Usage	: $map->add_element($marker)
	Function: Add a Bio::Map::MappableI object to the Map
	Returns : none
	Args	: Bio::Map::MappableI object
	Notes	: It is strongly recommended that you use a
		  Bio::Map::LinkagePosition as the position in any
		  Bio::Map::Mappable that you create to place on this
		  map. Using some other Bio::Map::Position might work but might
		  be unpredictable.
		  N.B. I've added Bio::Map::OrderedPosition which should achieve
		       similar things from LinkagePosition and will work for
		       RH markers too.

perl v5.14.2							    2012-03-02						 Bio::Map::LinkageMap(3pm)