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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:

   http://bugzilla.open-bio.org/
 
 

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    :