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


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

        # done!


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.


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AUTHOR - Chad Matsalla



Lincoln Stein Heikki Lehvaslaiho Jason Stajich


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


 Title   : new
 Usage   : my $linkage_map = new Bio::Map::LinkageMap();
 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


 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
           undef if length is not calculateable
 Args    : None.


 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.


 Title   : each_element
 Usage   : my @elements = $map->each_element;
 Function: Retrieves all the elements in a map
 Returns : An array containing MappableI objects.
 Args    : None.
 Notes   : This is a useless concept in the context of a linkage map but is
        included if you want a list of all of the marker names on the map.

implemented by Bio::Map::SimpleMap


 Title   : name($new_name)
 Usage   : my $name = $map->name($new_name) _or_
           my $length = $map->name()
 Function: Get/set the name of the map.
 Returns : The current name of the map.
 Args    : If provided, the name of the map is set to $new_name.


 Title   : species
 Usage   : my $species = $map->species;
 Function: Get/Set Species for a map
 Returns : Bio::Species object
 Args    : (optional) Bio::Species


 Title   : units
 Usage   : $map->units('cM');
 Function: Get/Set units for a map
 Returns : units for a map
 Args    : units for a map (string)


 Title   : type
 Usage   : my $type = $map->type
 Function: Get/Set Map type
 Returns : String coding map type
 Args    : (optional) string


 Title   : unique_id
 Usage   : my $id = $map->unique_id;
 Function: Get/Set the unique ID for this map
 Returns : a unique identifier
 Args    : [optional] new identifier to set