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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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NAME

Bio::EnsEMBL::MicroRNA - A class representing a microRNA product of a transcript

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();

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

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

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

_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