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 $map->add_element($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.

Mailing Lists
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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email bioinformatics1@dieselwurks.com Lincoln Stein lstein@cshl.org Heikki Lehvaslaiho heikki@ebi.ac.uk Jason Stajich jason@bioperl.org 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 = 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

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 undef 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. =cut #' sub _add_element { my ($self,$marker) = @_; my $o_position = $marker->position(); $self->debug( "marker position is ". $marker->position()); # print("add_element: \$o_position is $o_position\n"); # print("add_element: \$marker is $marker\n"); my $position; unless ( $o_position->isa('Bio::Map::LinkagePosition') || $o_position->isa('Bio::Map::OrderedPosition') ) { $self->warn("You really should use a Linkage Position for this object. This insures that there is only one position. Trying anyway..."); my @p = ( $o_position->each_position_value($self)); $position = shift @p; if( ! defined $position ) { $self->throw("This marker ($marker) does not have a position in this map ($self)"); } } else { $position = $o_position->order; } if ($self->{'_elements'}[$position]) { $self->warn("Replacing the marker in position $position because in a linkage map the position is a key."); } $self->{'_elements'}[$position] = $marker; }

each_element
Title : each_element Usage : my @elements = $map->each_element; Function: Retrieves all the elements in a map _ordered_. 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

name($new_name)
Title : name($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.

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

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

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

unique_id
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