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Bio::EnsEMBL::Funcgen::ProbeSet Class Reference
Inheritance diagram for Bio::EnsEMBL::Funcgen::ProbeSet:

List of all members.


Class Summary

Synopsis

 use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Funcgen::ProbeSet;


 my $reg = Bio::EnsEMBL::Registry-\>load_adaptors_from_db(-host    =\> 'ensembldb.ensembl.org',
                                                         -user    =\> 'anonymous');

 my $pset_adaptor = $reg-\>get_adaptor($species, 'funcgen', 'ProbeSet');

 ### Creating/storing a ProbeSet ###

 my $probe_set = Bio::EnsEMBL::Funcgen::ProbeSet-\>new(-NAME          =\> 'ProbeSet-1',
                                                      -SIZE          =\> 1,
                                                      -FAMILY        =\> "ENCODE REGIONS",#optional
                                                     );

 $pset_adaptor-\>store($probe_set);


 ### Fetching associated transcripts ###
 # Generated by the Ensembl array mapping pipeline

 my @dbentries     = @{$probe_set-\>fetch_all_Transcript_DBEntries};
 my $trans_adaptor = $reg-\>get_adpator($species, 'core', 'Transcript');

 foreach my $dbe(@dbentries){

    my $tx = $trans_adaptor-\>fetch_by_stable_id($dbe-\>primary_id);
   
    #Print the transcript info and the linkage annotation
    print $tx-\>stable_id."\t".$probe_set-\>name.' '.$dbe-\>linkage_annotation."\n";
 }

 #Alternatively these annotations are also available in a transcript centric manner
 #using the ProbeSetAdaptor

Description

A ProbeSet object represents a set of probes on a microarray. The
data (currently the name, size, and family) are stored in the probe_set 
table. ProbeSets are only really relevant for Affy probes, or when 
avaliable these will be analagous to Nimblegen feature sets.
For Affy arrays, a probeset can be part of more than one array, containing unique
probes.
#Need to rewrite this bit
#Something about array_chip_id i.e. experimental validation etc
On each Affy array the probe has a slightly different name. For
example, two different complete names for the same probe might be
DrosGenome1:AFFX-LysX-5_at:535:35; and Drosophila_2:AFFX-LysX-5_at:460:51;. In
the database, these two probes will have the same probe_id. Thus the same
Affy probe can have a number of different names and complete names depending on
which array it is on.
 

Definition at line 69 of file ProbeSet.pm.

Available Methods

public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public void add_DBEntry ()
public void add_status ()
public ARRAYREF associated_feature_types ()
public Int dbID ()
public String family ()
public Listref get_all_Arrays ()
public get_all_DAS_Features ()
public Listref get_all_DBEntries ()
public Listref get_all_Gene_DBEntries ()
public get_all_ProbeFeatures ()
public Listref get_all_Probes ()
public LISTREF get_all_states ()
public Listref get_all_Transcript_DBEntries ()
public Arrayref get_all_UnmappedObjects ()
public BOOLEAN has_status ()
public is_displayable ()
public Boolean is_stored ()
public String name ()
public
Bio::EnsEMBL::Funcgen::ProbeSet 
new ()
public Int size ()

Method Documentation

public void Bio::EnsEMBL::Funcgen::Storable::add_DBEntry ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBEntry $dbe
               The dbEntry to be added
  Example    : my $dbe = Bio::EnsEMBL::DBEntry->new(...);
               $transcript->add_DBEntry($dbe);
  Description: Associates a DBEntry with this object. Note that adding
               DBEntries will prevent future lazy-loading of DBEntries for this
               storable (see get_all_DBEntries).
  Returntype : none
  Exceptions : thrown on incorrect argument type
  Caller     : general
  Status     : Stable
 
Code:
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public void Bio::EnsEMBL::Funcgen::Storable::add_status ( ) [inherited]
  Example    : $ec->add_state('DISPLAYABLE');
  Description: Adds a state to a new or previously stored Storable
  Returntype : None
  Exceptions : Throws if no status supplied
  Caller     : general
  Status     : At risk
 
Code:
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public ARRAYREF Bio::EnsEMBL::Funcgen::Storable::associated_feature_types ( ) [inherited]
  Example    : my @associated_ftypes = @{$feature->associated_feature_types()};
  Description: Getter/Setter for other associated FeatureTypes.
  Returntype : ARRAYREF of Bio::EnsEMBL::Funcgen:FeatureType objects
  Exceptions : None
  Caller     : General
  Status     : At risk
 
Code:
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public String Bio::EnsEMBL::Funcgen::ProbeSet::family ( )
  Arg [1]    : (optional) string - family
  Example    : my $family = $probe->family();
  Description: Getter and setter of family attribute for ProbeSet
               objects. e.g. EXPERIMENTAL or CONTROL
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public Listref Bio::EnsEMBL::Funcgen::ProbeSet::get_all_Arrays ( )
  Args       : None
  Example    : my $arrays = $probeset->get_all_Arrays();
  Description: Returns all arrays that this probeset is part of. Only works if the
               probedet was retrieved from the database or created using
			   add_Array_probename.
  Returntype : Listref of Bio::EnsEMBL::Funcgen::Array objects
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public Listref Bio::EnsEMBL::Funcgen::Storable::get_all_DBEntries ( ) [inherited]
  Arg[1]     : string - External DB name e.g. ensembl_core_Gene
  Arg[2]     : string - External DB type 
  Example    : my @dbentries = @{ $set_feature->get_all_DBEntries };
  Description: Retrieves DBEntries (xrefs) for this SetFeature.  
               This does _not_ include the corresponding translations 
               DBEntries (see get_all_DBLinks).
               This method will attempt to lazy-load DBEntries from a
               database if an adaptor is available and no DBEntries are present
               on the SetFeature (i.e. they have not already been added or 
               loaded).
  Returntype : Listref of Bio::EnsEMBL::DBEntry objects
  Exceptions : none
  Caller     : general, get_all_DBLinks
  Status     : Stable - at risk move to storable
 
Code:
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public Listref Bio::EnsEMBL::Funcgen::Storable::get_all_Gene_DBEntries ( ) [inherited]
  Example    : my @gene_dbentries = @{ $storable->get_all_Gene_DBEntries };
  Description: Retrieves Ensembl Gene DBEntries (xrefs) for this Storable.  
               This does _not_ include the corresponding translations 
               DBEntries (see get_all_DBLinks).
               This method will attempt to lazy-load DBEntries from a
               database if an adaptor is available and no DBEntries are present
               on the transcript (i.e. they have not already been added or 
               loaded).
  Returntype : Listref of Bio::EnsEMBL::DBEntry objects
  Exceptions : none
  Caller     : general
  Status     : at risk
 
Code:
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public Bio::EnsEMBL::Funcgen::ProbeSet::get_all_ProbeFeatures ( )

Undocumented method

Code:
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public Listref Bio::EnsEMBL::Funcgen::ProbeSet::get_all_Probes ( )
  Args       : None
  Example    : my @probes = @{$probeset->get_all_Probes();
  Description: Returns all probes belonging to this ProbeSet
  Returntype : Listref of Bio::EnsEMBL::Funcgen::Probe objects
  Exceptions : None
  Caller     : General
  Status     : At Risk
 
Code:
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public LISTREF Bio::EnsEMBL::Funcgen::Storable::get_all_states ( ) [inherited]
  Example    : my @ec_states = @{$experimental_chip->get_all_states()};
  Description: Retrieves all states from DB and merges with current states array
  Returntype : LISTREF
  Exceptions : None
  Caller     : general
  Status     : At risk
 
Code:
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public Listref Bio::EnsEMBL::Funcgen::Storable::get_all_Transcript_DBEntries ( ) [inherited]
  Arg[0]     : optional - Bio::EnsEMBL::Transcript to filter DBEntries on.
  Example    : my @transc_dbentries = @{ $set_feature->get_all_Transcript_DBEntries };
  Description: Retrieves ensembl Transcript DBEntries (xrefs) for this Storable.  
               This does _not_ include the corresponding translations 
               DBEntries (see get_all_DBLinks).
               This method will attempt to lazy-load DBEntries from a
               database if an adaptor is available and no DBEntries are present
               on the Storable (i.e. they have not already been added or 
               loaded).
  Returntype : Listref of Bio::EnsEMBL::DBEntry objects
  Exceptions : none
  Caller     : general
  Status     : at risk
 
Code:
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public Arrayref Bio::EnsEMBL::Funcgen::Storable::get_all_UnmappedObjects ( ) [inherited]
  Example    : my @uos = @{$storable->get_all_UnmappedObjects };
  Description: Retrieves UnamappedObjects for this Storable.
  Returntype : arrayref of Bio::EnsEMBL::UnmappedObject objects
  Exceptions : none
  Caller     : general
  Status     : At risk - move to Bio::Ensembl::Storable?
 
Code:
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public BOOLEAN Bio::EnsEMBL::Funcgen::Storable::has_status ( ) [inherited]
  Arg [1]    : string - status e.g. IMPORTED, DISPLAYABLE
  Example    : if($experimental_chip->has_status('IMPORTED'){ ... skip import ... };
  Description: Tests whether storable has a given status
  Returntype : BOOLEAN
  Exceptions : Throws if not status is provided
  Caller     : general
  Status     : At risk
 
Code:
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public Bio::EnsEMBL::Funcgen::Storable::is_displayable ( ) [inherited]

Undocumented method

Code:
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public String Bio::EnsEMBL::Funcgen::ProbeSet::name ( )
  Arg [1]    : string - aprobeset name
  Example    : my $probesetname = $probeset->name('probeset-1');
  Description: Getter/Setter for the name attribute of ProbeSet objects.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public Bio::EnsEMBL::Funcgen::ProbeSet Bio::EnsEMBL::Funcgen::ProbeSet::new ( )
  Arg [-NAME]           : string - probeset name
  Arg [-SIZE]           : int - probe set size
        Will be the same for all probes sets if same probe set
		is on multiple arrays.
  Arg [-FAMILY]         : string - probe set family, generic descriptor for probe set e.g. ENCODE REGIONS, RANDOM
        Will be the same for all probes sets if same probe set is on multiple arrays.
  Example    : my $probeset = Bio::EnsEMBL::Funcgen::ProbeSet->new(
                   -NAME          => 'ProbeSet-1',
				   -SIZE          => 1,
                   -FAMILY        => "ENCODE_REGIONS",
               );
  Description: Creates a new Bio::EnsEMBL::Funcgen::ProbeSet object.
  Returntype : Bio::EnsEMBL::Funcgen::ProbeSet
  Exceptions : Throws if not supplied with probeset name and array chip id(s)
  Caller     : General
  Status     : Medium Risk
 
Code:
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Reimplemented from Bio::EnsEMBL::Funcgen::Storable.

public Int Bio::EnsEMBL::Funcgen::ProbeSet::size ( )
  Arg [1]    : (optional) int - probeset size
  Example    : my $probeset_size = $probeset->size();
  Description: Getter and setter of probeset size attribute for ProbeSet
               objects.
  Returntype : int
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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The documentation for this class was generated from the following file: