debian man page for bio::phenotype::correlate

Bio::Phenotype::Correlate(3pm)				User Contributed Perl Documentation			    Bio::Phenotype::Correlate(3pm)

NAME
       Bio::Phenotype::Correlate - Representation of a correlating phenotype in a given species

SYNOPSIS
	 use Bio::Phenotype::Correlate;

	 $co = Bio::Phenotype::Correlate->new( -name	    => "4(Tas1r3)",
					       -description => "mouse correlate of human phenotype MIM 605865",
					       -species     => $mouse,
					       -type	    => "homolog",
					       -comment     => "type=homolog is putative" );

	 print $co->name();
	 print $co->description();
	 print $co->species()->binomial();
	 print $co->type();
	 print $co->comment();

	 print $co->to_string();

DESCRIPTION
       This class models correlating phenotypes.  Its creation was inspired by the OMIM database where many human phenotypes have a correlating
       mouse phenotype. Therefore, this class is intended to be used together with a phenotype class.

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 one
       of the Bioperl mailing lists.  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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

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

AUTHOR
       Christian M. Zmasek

       Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com

       WWW:   http://monochrome-effect.net/

       Address:

	 Genomics Institute of the Novartis Research Foundation
	 10675 John Jay Hopkins Drive
	 San Diego, CA 92121

APPENDIX
       The rest of the documentation details each of the object methods.

   new
	Title	: new
	Usage	: $co = Bio::Phenotype::Correlate->new( -name	     => "4(Tas1r3)",
							-description => "mouse correlate of human phenotype MIM 605865",
							-species     => $mouse,
							-type	     => "homolog",
							-comment     => "type=homolog is putative" );
	Function: Creates a new Correlate object.
	Returns : A new Correlate object.
	Args	: -name        => a name or id
		  -description => a description
		  -species     => the species of this correlating phenotype [Bio::Species]
		  -type        => the type of correlation
		  -comment     => a comment

   init
	Title	: init()
	Usage	: $co->init();
	Function: Initializes this Correlate to all "".
	Returns :
	Args	:

   name
	Title	: name
	Usage	: $co->name( "4(Tas1r3)" );
		  or
		  print $co->name();
	Function: Set/get for the name or id of this Correlate.
	Returns : The name or id of this Correlate.
	Args	: The name or id of this Correlate (optional).

   description
	Title	: description
	Usage	: $co->description( "mouse correlate of human phenotype MIM 03923" );
		  or
		  print $co->description();
	Function: Set/get for the description of this Correlate.
	Returns : A description of this Correlate.
	Args	: A description of this Correlate (optional).

   species
	Title	: species
	Usage	: $co->species( $species );
		  or
		  $species = $co->species();
	Function: Set/get for the species of this Correlate.
	Returns : The Bio::Species of this Correlate [Bio::Species].
	Args	: The Bio::Species of this Correlate [Bio::Species] (optional).

   type
	Title	: type
	Usage	: $co->type( "homolog" );
		  or
		  print $co->type();
	Function: Set/get for the type of this Correlate.
	Returns : The type of this Correlate.
	Args	: The type of this Correlate (optional).

   comment
	Title	: comment
	Usage	: $co->comment( "doubtful" );
		  or
		  print $co->comment();
	Function: Set/get for an arbitrary comment about this Correlate.
	Returns : A comment.
	Args	: A comment (optional).

   to_string
	Title	: to_string()
	Usage	: print $co->to_string();
	Function: To string method for Correlate objects.
	Returns : A string representations of this Correlate.
	Args	:

perl v5.14.2							    2012-03-02					    Bio::Phenotype::Correlate(3pm)