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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METHODS
new
Title : new
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init
Title : init
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add_glyph
Title : add_glyph
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add_group
Title : add_group
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groups
Title : groups
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add_data
Title : add_data
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all_data
Title : all_data
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data
Title : data
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glyphs
Title : glyphs
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data_chunks
Title : data_chunks
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draw
Title : draw
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_recalculate_stats
Title : _recalculate_stats
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_parent_svg
Title : _parent_svg
Usage : $obj->_parent_svg($newval)
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Returns : value of _parent_svg (a scalar)
Args : on set, new value (a scalar or undef, optional)
_parent_group
Title : _parent_group
Usage : $obj->_parent_group($newval)
Function:
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Returns : value of _parent_group (a scalar)
Args : on set, new value (a scalar or undef, optional)
svg
Title : svg
Usage : $obj->svg($newval)
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Returns : value of svg (a scalar)
Args : on set, new value (a scalar or undef, optional)
xsize
Title : xsize
Usage : $obj->xsize($newval)
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Returns : value of xsize (a scalar)
Args : on set, new value (a scalar or undef, optional)
ysize
Title : ysize
Usage : $obj->ysize($newval)
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Returns : value of ysize (a scalar)
Args : on set, new value (a scalar or undef, optional)
xoffset
Title : xoffset
Usage : $obj->xoffset($newval)
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Returns : value of xoffset (a scalar)
Args : on set, new value (a scalar or undef, optional)
yoffset
Title : yoffset
Usage : $obj->yoffset($newval)
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Returns : value of yoffset (a scalar)
Args : on set, new value (a scalar or undef, optional)
xmin
Title : xmin
Usage : $obj->xmin($newval)
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Returns : value of xmin (a scalar)
Args : on set, new value (a scalar or undef, optional)
xmax
Title : xmax
Usage : $obj->xmax($newval)
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Returns : value of xmax (a scalar)
Args : on set, new value (a scalar or undef, optional)
ymin
Title : ymin
Usage : $obj->ymin($newval)
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Returns : value of ymin (a scalar)
Args : on set, new value (a scalar or undef, optional)
ymax
Title : ymax
Usage : $obj->ymax($newval)
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Returns : value of ymax (a scalar)
Args : on set, new value (a scalar or undef, optional)
xrange
Title : xrange
Usage : $obj->xrange($newval)
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Returns : value of xrange (a scalar)
yrange
Title : yrange
Usage : $obj->yrange($newval)
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Returns : value of yrange (a scalar)
stack
Title : stack
Usage : $obj->stack($newval)
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Returns : value of stack (a scalar)
Args : on set, new value (a scalar or undef, optional)
perl v5.10.0 2009-01-07 Frame(3pm)