| Bio::Map::CytoMarker(3pm) | User Contributed Perl Documentation | Bio::Map::CytoMarker(3pm) |
Bio::Map::CytoMarker - An object representing a marker.
$o_usat = Bio::Map::CytoMarker->new(-name=>'Chad Super Marker 2',
-position => $pos);
This object handles markers with a position in a cytogenetic map known. This marker will have a name and a position.
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
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.
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
Email heikki-at-bioperl-dot-org
Chad Matsalla bioinformatics1@dieselwurks.com Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org Sendu Bala bix@sendu.me.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
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.
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
| 2018-10-27 | perl v5.26.2 |