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Bio::Map::LinkageMap(3User Contributed Perl DocumentatiBio::Map::LinkageMap(3)

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://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08	       Bio::Map::LinkageMap(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Chad Matsalla | CONTRIBUTORS | APPENDIX

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