NAME
Bio::Phenotype::Phenotype - A class for modeling phenotypes
SYNOPSIS
#get Bio::Phenotype::PhenotypeI somehow
print $phenotype->name(), "\n";
print $phenotype->description(), "\n";
my @keywords = ( "achondroplasia", "dwarfism" );
$phenotype->add_keywords( @keywords );
foreach my $keyword ( $phenotype->each_keyword() ) {
print $keyword, "\n";
}
$phenotype->remove_keywords();
foreach my $gene_symbol ( $phenotype->each_gene_symbol() ) {
print $gene_symbol, "\n";
}
foreach my $corr ( $phenotype->each_Correlate() ) {
# Do something with $corr
}
foreach my $var ( $phenotype->each_Variant() ) {
# Do something with $var (mutation)
}
foreach my $measure ( $phenotype->each_Measure() ) {
# Do something with $measure
}DESCRIPTION
This superclass implements common methods for classes modelling phenotypes. Bio::Phenotype::OMIM::OMIMentry is an example of an instantiable phenotype class (the design of this interface was partially guided by the need to model OMIM entries). Please note. This class provides methods to associate mutations (methods "each_Variant", ...) and genotypes (methods "each_Genotype", ...) with phenotypes. Yet, these aspects might need some future enhancements, especially since there is no "genotype" class yet.
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 lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing listsReporting 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@gnf.org or cmzmasek@yahoo.com
WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : $obj = Bio::Phenotype::Phenotype->new( -name => "XY",
-description => "This is ..." );
Function: Creates a new Phenotype object.
Returns : A new Phenotype object.
Args : -name => the name
-description => the description of this phenotype
-species => ref to the the species
-comment => a comment init
Title : init()
Usage : $obj->init();
Function: Initializes this OMIMentry to all "" and empty lists.
Returns :
Args :name
Title : name
Usage : $obj->name( "r1" );
or
print $obj->name();
Function: Set/get for the name or id of this phenotype.
Returns : A name or id [scalar].
Args : A name or id [scalar] (optional).description
Title : description
Usage : $obj->description( "This is ..." );
or
print $obj->description();
Function: Set/get for the description of this phenotype.
Returns : A description [scalar].
Args : A description [scalar] (optional).species
Title : species
Usage : $obj->species( $species );
or
$species = $obj->species();
Function: Set/get for the species of this phenotype.
Returns : A species [Bio::Species].
Args : A species [Bio::Species] (optional).comment
Title : comment
Usage : $obj->comment( "putative" );
or
print $obj->comment();
Function: Set/get for a comment about this phenotype.
Returns : A comment [scalar].
Args : A comment [scalar] (optional).each_gene_symbol
Title : each_gene_symbol()
Usage : @gs = $obj->each_gene_symbol();
Function: Returns a list of gene symbols [scalars, most likely Strings]
associated with this phenotype.
Returns : A list of scalars.
Args :add_gene_symbols
Title : add_gene_symbols
Usage : $obj->add_gene_symbols( @gs );
or
$obj->add_gene_symbols( $gs );
Function: Pushes one or more gene symbols [scalars, most likely Strings]
into the list of gene symbols.
Returns :
Args : scalar(s).remove_gene_symbols
Usage : $obj->remove_gene_symbols();
Function: Deletes (and returns) the list of gene symbols [scalars,
most likely Strings] associated with this phenotype.
Returns : A list of scalars.
Args :each_Variant
Title : each_Variant()
Usage : @vs = $obj->each_Variant();
Function: Returns a list of Bio::Variation::VariantI implementing objects
associated with this phenotype.
This is for representing the actual mutation(s) causing this
phenotype.
{* The "variants" data member and its methods will/might need to be
changed/improved in one way or another, CZ 09/06/02 *}
Returns : A list of Bio::Variation::VariantI implementing objects.
Args :add_Variants
Usage : $obj->add_Variants( @vs );
or
$obj->add_Variants( $v );
Function: Pushes one or more Bio::Variation::VariantI implementing objects
into the list of Variants.
Returns :
Args : Bio::Variation::VariantI implementing object(s).remove_Variants
Title : remove_Variants
Usage : $obj->remove_Variants();
Function: Deletes (and returns) the list of Bio::Variation::VariantI implementing
objects associated with this phenotype.
Returns : A list of Bio::Variation::VariantI implementing objects.
Args :each_Reference
Title : each_Reference()
Usage : @refs = $obj->each_Reference();
Function: Returns a list of Bio::Annotation::Reference objects
associated with this phenotype.
Returns : A list of Bio::Annotation::Reference objects.
Args :add_References
Title : add_References
Usage : $obj->add_References( @refs );
or
$obj->add_References( $ref );
Function: Pushes one or more Bio::Annotation::Reference objects
into the list of References.
Returns :
Args : Bio::Annotation::Reference object(s).remove_References
Title : remove_References()
Usage : $obj->remove_References();
Function: Deletes (and returns) the list of Bio::Annotation::Reference objects
associated with this phenotype.
Returns : A list of Bio::Annotation::Reference objects.
Args :each_CytoPosition
Title : each_CytoPosition()
Usage : @cps = $obj->each_CytoPosition();
Function: Returns a list of Bio::Map::CytoPosition objects
associated with this phenotype.
Returns : A list of Bio::Map::CytoPosition objects.
Args :add_CytoPositions
Title : add_CytoPositions
Usage : $obj->add_CytoPositions( @cps );
or
$obj->add_CytoPositions( $cp );
Function: Pushes one or more Bio::Map::CytoPosition objects
into the list of CytoPositions.
Returns :
Args : Bio::Map::CytoPosition object(s).remove_CytoPositions
Title : remove_CytoPositions
Usage : $obj->remove_CytoPositions();
Function: Deletes (and returns) the list o fBio::Map::CytoPosition objects
associated with this phenotype.
Returns : A list of Bio::Map::CytoPosition objects.
Args :each_Correlate
Title : each_Correlate()
Usage : @corrs = $obj->each_Correlate();
Function: Returns a list of Bio::Phenotype::Correlate objects
associated with this phenotype.
(Correlates are correlating phenotypes in different species;
inspired by mouse correlates of human phenotypes in the OMIM
database.)
Returns : A list of Bio::Phenotype::Correlate objects.
Args :add_Correlates
Title : add_Correlates
Usage : $obj->add_Correlates( @corrs );
or
$obj->add_Correlates( $corr );
Function: Pushes one or more Bio::Phenotype::Correlate objects
into the list of Correlates.
Returns :
Args : Bio::Phenotype::Correlate object(s).remove_Correlates
Title : remove_Correlates
Usage : $obj->remove_Correlates();
Function: Deletes (and returns) the list of Bio::Phenotype::Correlate objects
associated with this phenotype.
Returns : A list of Bio::Phenotype::Correlate objects.
Args :each_Measure
Title : each_Measure()
Usage : @ms = $obj->each_Measure();
Function: Returns a list of Bio::Phenotype::Measure objects
associated with this phenotype.
(Measure is for biochemically defined phenotypes
or any other types of measures.)
Returns : A list of Bio::Phenotype::Measure objects.
Args :add_Measures
Title : add_Measures
Usage : $obj->add_Measures( @ms );
or
$obj->add_Measures( $m );
Function: Pushes one or more Bio::Phenotype::Measure objects
into the list of Measures.
Returns :
Args : Bio::Phenotype::Measure object(s).remove_Measures
Title : remove_Measures
Usage : $obj->remove_Measures();
Function: Deletes (and returns) the list of Bio::Phenotype::Measure objects
associated with this phenotype.
Returns : A list of Bio::Phenotype::Measure objects.
Args :each_keyword
Title : each_keyword()
Usage : @kws = $obj->each_keyword();
Function: Returns a list of key words [scalars, most likely Strings]
associated with this phenotype.
Returns : A list of scalars.
Args :add_keywords
Title : add_keywords
Usage : $obj->add_keywords( @kws );
or
$obj->add_keywords( $kw );
Function: Pushes one or more keywords [scalars, most likely Strings]
into the list of key words.
Returns :
Args : scalar(s).remove_keywords
Title : remove_keywords
Usage : $obj->remove_keywords();
Function: Deletes (and returns) the list of key words [scalars,
most likely Strings] associated with this phenotype.
Returns : A list of scalars.
Args :each_DBLink
Title : each_DBLink()
Usage : @dbls = $obj->each_DBLink();
Function: Returns a list of Bio::Annotation::DBLink objects
associated with this phenotype.
Returns : A list of Bio::Annotation::DBLink objects.
Args :add_DBLink
Title : add_DBLink
Usage : $obj->add_DBLinks( @dbls );
or
$obj->add_DBLinks( $dbl );
Function: Pushes one or more Bio::Annotation::DBLink objects
into the list of DBLinks.
Returns :
Args : Bio::Annotation::DBLink object(s).remove_DBLinks
Title : remove_DBLinks
Usage : $obj->remove_DBLinks();
Function: Deletes (and returns) the list of Bio::Annotation::DBLink objects
associated with this phenotype.
Returns : A list of Bio::Annotation::DBLink objects.
Args :each_Genotype
Title : each_Reference()
Usage : @gts = $obj->each_Reference();
Function: Returns a list of "Genotype" objects
associated with this phenotype.
{* the "genotypes" data member and its methods certainly will/needs to be
changed/improved in one way or another since there is
no "Genotype" class yet, CZ 09/06/02 *}
Returns : A list of "Genotype" objects.
Args :add_Genotypes
Title : add_Genotypes
Usage : $obj->add_Genotypes( @gts );
or
$obj->add_Genotypes( $gt );
Function: Pushes one or more "Genotypes"
into the list of "Genotypes".
Returns :
Args : "Genotypes(s)".remove_Genotypes
Title : remove_Genotypes
Usage : $obj->remove_Genotypes();
Function: Deletes (and returns) the list of "Genotype" objects
associated with this phenotype.
Returns : A list of "Genotype" objects.
Args :_check_ref_type
Title : _check_ref_type
Usage : $self->_check_ref_type( $value, "Bio::Annotation::DBLink" );
Function: Checks for the correct type.
Returns :
Args : The value to be checked, the expected class.