go::model::graphnodeinstance(3pm) [debian man page]
GO::Model::GraphNodeInstance(3pm) User Contributed Perl Documentation GO::Model::GraphNodeInstance(3pm)NAME
GO::Model::GraphNodeInstance - a graph node located in a tree
SYNOPSIS
$it = $graph->create_iterator;
# returns a GO::Model::GraphIterator object
while (my $ni = $it->next_node_instance) {
$depth = $ni->depth;
$term = $ni->term;
$reltype = $ni->parent_rel->type;
printf
"%s %8s Term = %s (%s) // depth=%d
",
"----" x $depth,
$reltype,
$term->name,
$term->public_acc,
$depth;
}
DESCRIPTION
see GO::Model::Graph
term
Usage -
Returns - GO::Model::Term
Args -
see GO::Model::Term
depth
Usage -
Returns - int
Args -
parent_rel
Usage -
Returns - GO::Model::Relationship
Args -
see GO::Model::Relationship
perl v5.14.2 2010-05-12 GO::Model::GraphNodeInstance(3pm)
Check Out this Related Man Page
GO::Model::Association(3pm) User Contributed Perl Documentation GO::Model::Association(3pm)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)
",
$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
perl v5.14.2 2013-02-07 GO::Model::Association(3pm)
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