Christopher Fields > BioPerl-1.6.923 > Bio::Map::CytoMarker

Download:
BioPerl-1.6.923.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  11
Open  4
View/Report Bugs
Source   Latest Release: BioPerl-1.6.924

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://redmine.open-bio.org/projects/bioperl/

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
syntax highlighting: