Bio::EnsEMBL::Map::Qtl Class Reference

Inheritance diagram for Bio::EnsEMBL::Map::Qtl:

List of all members.

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Class Summary

Synopsis

Description

Represents a Qtl in the EnsEMBL database. A quantitative trait locus is
defined by three markers, two flanking and one peak (optional) marker.
Its a region (or more often a group of regions) which is likely to
affect the phenotype (trait) described in this Qtl.

Definition at line 18 of file Qtl.pm.

Available Methods
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public void	add_synonym ()
public Int	dbID ()
public Bio::EnsEMBL::Map::Marker	flank_marker_1 ()
public Bio::EnsEMBL::Map::Marker	flank_marker_2 ()
public	get_all_DAS_Features ()
public Bio::EnsEMBL::Map::QtlFeature	get_QtlFeatures ()
public Hashref	get_synonyms ()
public Boolean	is_stored ()
public Float	lod_score ()
public Bio::EnsEMBL::Map::Qtl	new ()
public Bio::EnsEMBL::Map::Marker	peak_marker ()
public	source_database ()
public	source_primary_id ()
public String	trait ()

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Method Documentation

public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor

(

)

[inherited]

  Arg [1]    : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
  Example    : none
  Description: get/set for this objects Adaptor
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable

Code:

public void Bio::EnsEMBL::Map::Qtl::add_synonym

(

)

  Arg [1]    : string $source
               The source of the synonym
  Arg [2]    : string $identifier
               The identifier from this source
  Example    : $qtl->add_synonym('rat genome database', '65516');
  Description: Adds a synonym to this qtl
  Returntype : none
  Exceptions : thrown if arguments are not provided
  Caller     : general
  Status     : stable

Code:

public Int Bio::EnsEMBL::Storable::dbID

(

)

[inherited]

  Arg [1]    : int $dbID
  Example    : none
  Description: getter/setter for the database internal id
  Returntype : int
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable

Code:

Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

public Bio::EnsEMBL::Map::Marker Bio::EnsEMBL::Map::Qtl::flank_marker_1

(

)

  Arg [1]    : Bio::EnsEMBL::Map::Marker $flank_marker_1
               One flanking marker of the interest region, the two flanking
               markers define the region
  Example    : none
  Description: Getter/Setter attribute flanking_marker_1
  Returntype : Bio::EnsEMBL::Map::Marker
  Exceptions : none
  Caller     : general
  Status     : stable

Code:

public Bio::EnsEMBL::Map::Marker Bio::EnsEMBL::Map::Qtl::flank_marker_2

(

)

  Arg [1]    : Bio::EnsEMBL::Map::Marker $flank_marker_2
               One flanking marker of the interest region, the two flanking
               markers define the region
  Example    : none
  Description: Getter/Setter attribute flanking_marker_2
  Returntype : Bio::EnsEMBL::Map::Marker
  Exceptions : none
  Caller     : general
  Status     : stable

Code:

public Bio::EnsEMBL::Storable::get_all_DAS_Features

(

)

[inherited]

Undocumented method

Code:

Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.

public Bio::EnsEMBL::Map::QtlFeature Bio::EnsEMBL::Map::Qtl::get_QtlFeatures

(

)

  Args       : none
  Example    : none
  Description: return the qtl feature which is associated with this
               Qtl. It comes in chromosomal slice coordinates. There can 
               only be one.
  Returntype : Bio::EnsEMBL::Map::QtlFeature
  Exceptions : only works with adaptored Qtls
  Caller     : general
  Status     : stable

Code:

public Hashref Bio::EnsEMBL::Map::Qtl::get_synonyms

(

)

  Arg [1]    : none
  Example    :
     foreach my $source ($keys %{$qtl->get_synonyms}) {
       print $source . ':'. $qtl->get_synonyms->{$source};
     }
  Description: Returns a hashref of synonyms keyed on their source name 
  Returntype : hashref of synonyms keyed on their source name
  Exceptions : none
  Caller     : general
  Status     : stable

Code:

public Boolean Bio::EnsEMBL::Storable::is_stored

(

)

[inherited]

  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection 
             : or Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    : do_something if($object->is_stored($db));
  Description: Returns true if this object is stored in the provided database.
               This works under the assumption that if the adaptor and dbID are
               set and the database of the adaptor shares the port, dbname and
               hostname with the provided database, this object is stored in
               that database.
  Returntype : 1 or 0
  Exceptions : throw if dbID is set but adaptor is not
               throw if adaptor is set but dbID is not
               throw if incorrect argument is passed
  Caller     : store methods
  Status     : Stable

Code:

public Float Bio::EnsEMBL::Map::Qtl::lod_score

(

)

  Arg [1]    : float $lod_score
               A score for the Qtl
  Example    : none
  Description: Getter/Setter for attribute lod_score
  Returntype : float
  Exceptions : none
  Caller     : general
  Status     : stable

Code:

public Bio::EnsEMBL::Map::Qtl Bio::EnsEMBL::Map::Qtl::new

(

)

  Arg [1]    : int $dbID
  Arg [2]    : Bio::EnsEMBL::Map::DBSQL::QtlAdaptor $adaptor
  Arg [3]    : Bio::EnsEMBL::Map::Marker $flank_marker_1
  Arg [4]    : Bio::EnsEMBL::Map::Marker $peak_marker
  Arg [5]    : Bio::EnsEMBL::Map::Marker $flank_marker_2
  Arg [6]    : string $trait
  Arg [7]    : float $lod_score
  Arg [8]    : hashref $synonyms
               A hashref with source keys and identifier values
  Example    : none
  Description: Creates a new Qtl object. Usually done by Adaptor
  Returntype : Bio::EnsEMBL::Map::Qtl
  Exceptions : none
  Caller     : general, DBSQL::QtlAdaptor, DBSQL::QtlFeatureAdaptor
  Status     : stable

Code:

Reimplemented from Bio::EnsEMBL::Storable.

public Bio::EnsEMBL::Map::Marker Bio::EnsEMBL::Map::Qtl::peak_marker

(

)

  Arg [1]    : Bio::EnsEMBL::Map::Marker $peak_marker
               an optional Marker which has the peak probablitity
               for this traits occurence
  Example    : none
  Description: Getter/Setter for attribute peak_marker
  Returntype : Bio::EnsEMBL::Map::Marker
  Exceptions : none
  Caller     : general
  Status     : stable

Code:

public Bio::EnsEMBL::Map::Qtl::source_database

(

)

This method is

Deprecated:
.  Use get_synonyms or add_synonym instead.

Code:

public Bio::EnsEMBL::Map::Qtl::source_primary_id

(

)

This method is

Deprecated:
. Use get_synonyms or add_synonym instead.

Code:

public String Bio::EnsEMBL::Map::Qtl::trait

(

)

  Arg [1]    : string $trait
               Phenotype of this Qtl
  Example    : none
  Description: Getter/Setter for the trait attribute
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : stable

Code:

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The documentation for this class was generated from the following file:

• Bio/EnsEMBL/Map/Qtl.pm