Bio::Map::CytoMarker(3)

NAME
Bio::Map::CytoMarker - An object representing a marker.

SYNOPSIS
  $o_usat = Bio::Map::CytoMarker->new(-name=>'Chad Super Marker 2',
                                 -position => $pos);

DESCRIPTION
This object handles markers with a positon in a cytogenetic map known. This marker will have a name and a 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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki Lehvaslaiho
Email heikki-at-bioperl-dot-org

CONTRIBUTORS
Chad Matsalla bioinformatics1@dieselwurks.com Lincoln Stein lstein@cshl.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 _

  Bio::Map::MarkerI methods

  get_position_object
 Title   : get_position_class
 Usage   : my $position = $marker->get_position_object();
 Function: To get an object of the default Position class
           for this Marker. Subclasses should redefine this method.
           The Position returned needs to be a L<Bio::Map::PositionI> with
                   -element set to self.
 Returns : L<Bio::Map::PositionI>
 Args    : none for an 'empty' PositionI object, optionally
           Bio::Map::MapI and value string to set the Position's -map and -value
           attributes.

  Comparison methods
The numeric values for cutogeneic loctions go from the p tip of chromosome 1, down to the q tip and similarly throgh consecutive chromosomes, through X and end the the q tip of X. See Bio::Map::CytoPosition::cytorange for more details.

  New methods

  get_chr
 Title   : get_chr
 Usage   : my $mychr = $marker->get_chr();
 Function: Read only method for the  chromosome string of the location.
           A shortcut to $marker->position->chr().
 Returns : chromosome value
 Args    : [optional] new chromosome value