Bio::Phenotype::OMIM::OMIMentryAllelicVariant(3pm) User Contributed Perl Documentation Bio::Phenotype::OMIM::OMIMentryAllelicVariant(3pm)
NAME
Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic variant of the OMIM database
SYNOPSIS
use Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
$av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number => ".0001",
-title => "ALCOHOL INTOLERANCE",
-symbol => "ALDH2*2",
-description => "The ALDH2*2-encoded ...",
-aa_ori => "GLU",
-aa_mut => "LYS",
-position => 487,
-additional_mutations => "IVS4DS, G-A, +1" );
DESCRIPTION
This class models the allelic variant of the OMIM database. This class is intended to be used together with a OMIM entry class.
FEEDBACK
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rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
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Reporting Bugs
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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 : $av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number => ".0001",
-title => "ALCOHOL INTOLERANCE",
-symbol => "ALDH2*2",
-description => "The ALDH2*2-encoded ...",
-aa_ori => "GLU",
-aa_mut => "LYS",
-position => 487,
-additional_mutations => "IVS4DS, G-A, +1" );
Function: Creates a new OMIMentryAllelicVariant object.
Returns : A new OMIMentryAllelicVariant object.
Args : -number => the OMIM allelic variant number
-title => the title
-symbol => a symbol
-description => a description
-aa_ori => the original amino acid
-aa_mut => the mutated amino acid
-position => the position of the mutation
-additional_mutations => free form description of additional mutations
init
Title : init()
Usage : $av->init();
Function: Initializes this OMIMentryAllelicVariant to all "".
Returns :
Args :
number
Title : number
Usage : $av->number( ".0001" );
or
print $av->number();
Function: Set/get for the OMIM allelic variant number of this
OMIMentryAllelicVariant.
Returns : The OMIM allelic variant number.
Args : The OMIM allelic variant number (optional).
title
Title : title
Usage : $av->title( "ALCOHOL INTOLERANCE" );
or
print $av->title();
Function: Set/get for the title of this OMIMentryAllelicVariant.
Returns : The title.
Args : The title (optional).
symbol
Title : symbol
Usage : $av->symbol( "ALDH2*2" );
or
print $av->symbol();
Function: Set/get for the symbol of this OMIMentryAllelicVariant.
Returns : A symbol.
Args : A symbol (optional).
description
Title : description
Usage : $av->description( "The ALDH2*2-encoded protein has a change ..." );
or
print $av->description();
Function: Set/get for the description of this OMIMentryAllelicVariant.
Returns : A description.
Args : A description (optional).
aa_ori
Title : aa_ori
Usage : $av->aa_ori( "GLU" );
or
print $av->aa_ori();
Function: Set/get for the original amino acid(s).
Returns : The original amino acid(s).
Args : The original amino acid(s) (optional).
aa_mut
Title : aa_mut
Usage : $av->aa_mut( "LYS" );
or
print $av->aa_mut();
Function: Set/get for the mutated amino acid(s).
Returns : The mutated amino acid(s).
Args : The mutated amino acid(s) (optional).
position
Title : position
Usage : $av->position( 487 );
or
print $av->position();
Function: Set/get for the position of the mutation.
Returns : The position of the mutation.
Args : The position of the mutation (optional).
additional_mutations
Title : additional_mutations
Usage : $av->additional_mutations( "1-BP DEL, 911T" );
or
print $av->additional_mutations();
Function: Set/get for free form description of (additional) mutation(s).
Returns : description of (additional) mutation(s).
Args : description of (additional) mutation(s) (optional).
to_string
Title : to_string()
Usage : print $av->to_string();
Function: To string method for OMIMentryAllelicVariant objects.
Returns : A string representations of this OMIMentryAllelicVariant.
Args :
perl v5.14.2 2012-03-02 Bio::Phenotype::OMIM::OMIMentryAllelicVariant(3pm)