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.\" ========================================================================
.\"
.IX Title "Bio::Map::LinkageMap 3pm"
.TH Bio::Map::LinkageMap 3pm "2017-01-15" "perl v5.24.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Map::LinkageMap \- A representation of a genetic linkage map.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 10
\&    use Bio::Map::LinkageMap;
\&        # create a new map
\&    my $map = Bio::Map::LinkageMap\->new(\-name => \*(AqChads Superterriffic Map\*(Aq,
\&                                      \-type => \*(AqLinkage\*(Aq,
\&                                      \-units=> \*(AqcM\*(Aq);
\&        # 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 => \*(AqSuuuperMarker\*(Aq,
\&                        \-position => $position);
\&        # place that marker on that map
\&    $map\->add_element($marker);
\&
\&        # done!
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Chad Matsalla"
.IX Header "AUTHOR - Chad Matsalla"
Email bioinformatics1@dieselwurks.com
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Lincoln Stein       lstein@cshl.org
Heikki Lehvaslaiho  heikki-at-bioperl-dot-org
Jason Stajich       jason@bioperl.org
Sendu Bala          bix@sendu.me.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 11
\& 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
.Ve
.SS "length"
.IX Subsection "length"
.Vb 7
\& Title   : length
\& Usage   : my $length = $map\->length();
\& Function: Retrieves the length of the map. In the case of a LinkageMap, the
\&               length is the sum of all marker distances.
\& Returns : An integer representing the length of this LinkageMap. Will return
\&               0 if length is not calculateable
\& Args    : None.
.Ve
.SS "add_element($marker)"
.IX Subsection "add_element($marker)"
.Vb 10
\& Title   : add_element($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\*(Aqve added Bio::Map::OrderedPosition which should achieve
\&                similar things from LinkagePosition and will work for
\&                RH markers too.
.Ve