Bio::Map::LinkageMap - A representation of a genetic linkage map.
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!
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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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : length Usage : my $length = $map->length(); Function: Retrieves the length of the map. In the case of a LinkageMap, the length is the sum of all marker distances. Returns : An integer representing the length of this LinkageMap. Will return 0 if length is not calculateable Args : None.
Title : add_element($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.