| GO::Model::Association(3pm) | User Contributed Perl Documentation | GO::Model::Association(3pm) |
GO::Model::Association - association between a GO term and a gene product
# 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};
}
Represents an association between a GO term (GO::Model::Term) and a gene product (GO::Model::GeneProduct)
Usage - Returns - Args -
Usage - $assoc->add_evidence($my_evid); Returns - Args - GO::Model::Evidence
Usage - my $ev_l = $assoc->evidence_list; Returns - Args -
gets/sets arrayref of GO::Model::Evidence
Usage - print $assoc->evidence_as_str Usage - print $assoc->evidence_as_str(1); #verbose Returns - Args - verbose
concatenates evcodes together, for display
Usage - if $assoc->has_evcode("IEA");
Returns - boolean
Args - evcode [string]
Usage - $assoc->remove_evcode("IEA");
Returns -
Args - evcode [string]
removes all evidence of the specified type from the association; useful for filtering
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 hierarchy:
TAS
IDA
IMP/IGI/IPI
ISS
NAS
see http://www.geneontology.org/GO.evidence.html
Usage - my $gp = $assoc->gene_product Returns - Args -
gets sets GO::Model::GeneProduct
Usage - Returns - Args -
Usage - Returns - Args -
gets/sets boolean representing whether this relationship is negated
Usage - Returns - Args -
Usage - Returns - Args -
gets/sets integer representing the date of the association (YYYYMMDD format)
Usage - Returns - Args -
gets/sets integer to indicate which associations go together
| 2021-01-09 | perl v5.32.0 |