Bio::EnsEMBL::MicroRNA Class Reference

Inheritance diagram for Bio::EnsEMBL::MicroRNA:

Public Member Functions
public Bio::EnsEMBL::MicroRNA	new ()
public Int	arm ()
public Hashref	summary_as_hash ()
protected void	_validate_arm_value ()
Public Member Functions inherited from Bio::EnsEMBL::RNAProduct
public Bio::EnsEMBL::RNAProduct	new ()
public void	add_Attributes ()
public void	add_DBEntry ()
public Int	cdna_end ()
public Int	cdna_start ()
public String	created_date ()
public String	display_id ()
public Int	end ()
public Bio::EnsEMBL::Exon	end_Exon ()
public Int	genomic_end ()
public Int	genomic_start ()
public Listref	get_all_Attributes ()
public Listref	get_all_DBEntries ()
public Listref	get_all_DBLinks ()
public Listref	get_all_object_xrefs ()
public Listref	get_all_xrefs ()
public String	modified_date ()
public Int	length ()
public void	load ()
public String	seq ()
public String	stable_id ()
public String	stable_id_version ()
public Int	start ()
public Bio::EnsEMBL::Exon	start_Exon ()
public Hashref	summary_as_hash ()
public void	synchronise_attributes ()
public Bio::EnsEMBL::Transcript	transcript ()
public String	type_code ()
public String	version ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

Description

A specialisation of Bio::EnsEMBL::RNAProduct describing
MicroRNAs. Mostly takes care of wrapping miRNA-specific RNAProduct
attributes in methods which make them look like ordinary class
members.

Synopsis

my $miR = Bio::EnsEMBL::MicroRNA->new(
  -SEQ_START => 36,
  -SEQ_END   => 58
);
 
# Stable-ID setter
$miR->stable_id('ENSS00090210');
 
# Get start and end position in the precursor transcript
my $start = $miR->start();
my $end = $miR->end();

Definition at line 32 of file MicroRNA.pm.

Member Function Documentation

_validate_arm_value()

protected void Bio::EnsEMBL::MicroRNA::_validate_arm_value

(

)

  Arg [1]    : int $arm which arm of the hairpin precursor this miRNA
               comes from
  Description: PRIVATE validates if its argument has one of the accepted
               values for specifying the miRNA hairpin arm.
  Returntype : none
  Exceptions : throw if the argument is out of bounds
  Caller     : internal
  Status     : Stable

Code:

arm()

public Int Bio::EnsEMBL::MicroRNA::arm

(

)

    Arg [1]     : (optional) int $arm which arm of the hairpin precursor
                  this miRNA comes from
    Example     :

$mirna_arm = $mirna->arm();
                 $mirna->arm(3);

    Description : Sets or returns the arm of the hairpin this miRNA comes
                  from. Accepted values are 3 and 5 for 3' and 5',
                  respectively.
    Return type : Integer
    Exceptions  : throw if setter is passed an incorrect value
                  or if multiple 'mirna_arm' attributes exist.
    Caller      : General
    Status      : Stable

Code:

new()

public Bio::EnsEMBL::MicroRNA Bio::EnsEMBL::MicroRNA::new

(

)

  Arg: [-ARM]         : which arm of the hairpin precursor this miRNA comes
                        from. Returns 3 and 5 for 3' and 5', respectively.
  Arg [...]           : Named arguments to superclass constructor
                        (see Bio::EnsEMBL::RNAProduct)
  Example    :

my $miR = Bio::EnsEMBL::MicroRNA->new(
                -SEQ_START => 36,
                -SEQ_END   => 58,
                -ARM       => 3
              );

  Description: Constructor.  Creates a new MicroRNA object
  Returntype : Bio::EnsEMBL::MicroRNA
  Exceptions : throw if ARM value is out of bounds
  Caller     : general
  Status     : In Development

Code:

summary_as_hash()

public Hashref Bio::EnsEMBL::MicroRNA::summary_as_hash

(

)

  Example       :

$mirna_summary = $mirna->summary_as_hash();

  Description   : Retrieves a textual summary of this MicroRNA.
                  Built on top of generic implementation in RNAProduct.
  Returns       : hashref of arrays of descriptive strings
  Status        : Intended for internal use

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/MicroRNA.pm