Ewan Birney

NAME

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

SYNOPSIS

  $o_usat = new Bio::Map::CytoMarker(-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/MailList.shtml  - About the mailing lists

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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR - Heikki Lehvaslaiho

Email heikki@ebi.ac.uk

CONTRIBUTORS

Chad Matsalla bioinformatics1@dieselwurks.com Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org

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 $pos = $marker->get_position_object();
 Function: To get an object of the default Position class
           for this Marker. Subclasses should redefine this method.
           The Position needs to be L<Bio::Map::PositionI>.
 Returns : L<Bio::Map::CytoPosition>
 Args    : none

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.

The numeric values for cytogenetic positions are ranges of type Bio::Range, so MarkerI type of operators (equals, less_than, greater_than) are not very meaningful, but they might be of some use combined with Bio::RangeI methods (overlaps, contains, equals, intersection, union). equals(), present in both interfaces is treated as a more precice RangeI method.

CytoMarker has a method get_chr which might turn out to be useful in this context.

The less_than and greater_than methods are implemented by comparing the end values of the range, so you better first check that markers do not overlap, or you get an opposite result than expected. The numerical values are not metric, so avarages are not meaningful.

Note: These methods always return a value. A false value (0) might mean that you have not set the position! Check those warnings.

Bio::Map::MarkerI comparison methods

tuple

 Title   : tuple
 Usage   : ($me, $you) = $self->_tuple($compare)
 Function: Utility method to extract numbers and test for missing values.
 Returns : two ranges or tuple of -1
 Args    : Bio::Map::MappableI or Bio::Map::PositionI

less_than

 Title   : less_than
 Usage   : if( $mappable->less_than($m2) ) ...
 Function: Tests if a position is less than another position
 Returns : boolean
 Args    : Bio::Map::MappableI  or Bio::Map::PositionI

greater_than

 Title   : greater_than
 Usage   : if( $mappable->greater_than($m2) ) ...
 Function: Tests if position is greater than another position
 Returns : boolean
 Args    : Bio::Map::MappableI or Bio::Map::PositionI

RangeI methods

equals

 Title   : equals
 Usage   : if( $mappable->equals($mapable2)) ...
 Function: Test if a position is equal to another position
 Returns : boolean
 Args    : Bio::Map::MappableI or Bio::Map::PositionI

overlaps

  Title    : overlaps
  Usage    : if($r1->overlaps($r2)) { do stuff }
  Function : tests if $r2 overlaps $r1
  Args     : a range to test for overlap with
  Returns  : true if the ranges overlap, false otherwise
  Inherited: Bio::RangeI

contains

  Title    : contains
  Usage    : if($r1->contains($r2) { do stuff }
  Function : tests wether $r1 totaly contains $r2
  Args     : a range to test for being contained
  Returns  : true if the argument is totaly contained within this range
  Inherited: Bio::RangeI

intersection

  Title    : intersection
  Usage    : ($start, $stop, $strand) = $r1->intersection($r2)
  Function : gives the range that is contained by both ranges
  Args     : a range to compare this one to
  Returns  : nothing if they do not overlap, or the range that they do overlap
  Inherited: Bio::RangeI::intersection

union

  Title    : union
  Usage    : ($start, $stop, $strand) = $r1->union($r2);
           : ($start, $stop, $strand) = Bio::Range->union(@ranges);
  Function : finds the minimal range that contains all of the ranges
  Args     : a range or list of ranges to find the union of
  Returns  : the range containing all of the ranges
  Inherited: Bio::RangeI::union

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 shotrcut to $marker->position->chr().
 Returns : chromosome value
 Args    : [optional] new chromosome value