Chris Mungall > go-perl-0.14 > GO::Model::Association;

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NAME ^

  GO::Model::Association;

SYNOPSIS ^

  # print all gene products associated with a GO::Model::Term
  my $assoc_l = $term->association_list;
  foreach my $assoc (@$assoc_l) {
    printf "gene product:%s %s %s (evidence: %s)\n",
      $assoc->gene_product->symbol,
      $assoc->is_not ? "IS NOT" : "IS",
      $term->name,
      map {$_->code} @{$assoc->evidence_list};
  }

DESCRIPTION ^

Represents an association between a GO term (GO::Model::Term) and a gene product (GO::Model::GeneProduct)

go_public_acc

  Usage   -
  Returns -
  Args    -

add_evidence

  Usage   - $assoc->add_evidence($my_evid);
  Returns -
  Args    - GO::Model::Evidence

evidence_list

  Usage   - my $ev_l = $assoc->evidence_list;
  Returns -
  Args    -

gets/sets arrayref of GO::Model::Evidence

evidence_as_str

  Usage   - print $assoc->evidence_as_str
  Usage   - print $assoc->evidence_as_str(1); #verbose
  Returns -
  Args    - verbose

concatenates evcodes together, for display

has_evcode

  Usage   - if $assoc->has_evcode("IEA");
  Returns - boolean
  Args    - evcode [string]

remove_evcode

  Usage   - $assoc->remove_evcode("IEA");
  Returns - 
  Args    - evcode [string]

removes all evidence of the specified type from the association; useful for filtering

evidence_score

  Usage   - my $score = $assoc->evidence_score
  Returns - 0 <= float <= 1
  Args    -

returns a score for the association based on the evidence;

This is an EXPERIMENTAL method; it may be removed in future versions.

The evidence fields can be thought of in a loose hierachy:

TAS IDA IMP/IGI/IPI ISS NAS

see http://www.geneontology.org/GO.evidence.html

gene_product

  Usage   - my $gp = $assoc->gene_product
  Returns -
  Args    -

gets sets GO::Model::GeneProduct

assigned_by

  Usage   -
  Returns -
  Args    -

is_not

  Usage   -
  Returns -
  Args    -

gets/sets boolean representing whether this relationship is negated

assocdate

  Usage   -
  Returns -
  Args    -

assocdate

  Usage   -
  Returns -
  Args    -

gets/sets integer representing the date of the association (YYYYMMDD format)

role_group

  Usage   -
  Returns -
  Args    -

gets/sets integer to indicate which associations go together

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