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)