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