Bio::Map::LinkageMap.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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.