Bio::Network::Interaction - describes a protein-protein interaction
# Add an interaction with some attributes use Bio::Network::Interaction; my $interx = Bio::Network::Interaction->new(-weight => $score, -id => $id); $gr->add_interaction(-nodes => [($node1,$node2)], -interaction => $interx); # Retrieve an interaction using an identifier my $interaction = $gr->get_interaction_by_id($id); my $id = $interaction->primary_id; my $wt = $interaction->weight; my @nodes = $interaction->nodes;
This class contains information about a bi-molecular interaction. At present it just contains data about a weight (optional) and an identifier. Subclasses could hold more specific information. A pair of nodes can have more than one Interaction object associated with it.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
Brian Osborne bosborne at alum.mit.edu Richard Adams firstname.lastname@example.org
Maintained by Brian Osborne
Name : new Purpose : Constructor for an Interaction object Usage : my $interx = Bio::Network::Interaction->new(-id => $id); Returns : A new Bio::Network::Interaction object Arguments : -id => interaction id -weight (optional) => weight score
Name : weight Purpose : Get or set a weight or score Usage : my $weight = $interx->weight() or $interx->weight(3) Returns : a number Arguments : Nothing or a number
Name : primary_id Purpose : Get or set the primary_id Usage : my $id = $interx->primary_id() or $interx->primary_id("SIB4") Returns : A string identifier Arguments : Nothing or an identifier
Name : nodes Purpose : Get the pair of nodes for an Interaction Usage : my $count = $interx->nodes or my @nodes = $interx->nodes Returns : Gets an array of 2 Nodes or a count of the number of Nodes Arguments : Notes : Getting a count of the number of Nodes in an Interaction will almost always return 2, but there is a formal possibility that a Node could interact with itself, returning 1
Title : annotation Usage : my $annotation = $ix->annotation or $ix->annotation($annotation) Function: Gets or sets the annotation Returns : Bio::AnnotationCollectionI object Args : None or Bio::AnnotationCollectionI object
Name : object_id Purpose : Alias to primary_id Usage : my $id = $edge->object_id() Notes : Deprecated