GO::Model::Association.3pm

Langue: en

Autres versions - même langue

Version: 2009-11-06 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

   GO::Model::Association - association between a GO term and a gene product
 
 

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