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://github.com/bioperl/bioperl-live/issues
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).
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 :