methods.interologs
Class InterologsCalculator

java.lang.Object
  extended by methods.interologs.InterologsCalculator

public class InterologsCalculator
extends Object

Calculates interologs from a given set of binary interactions and a (homology) mapping between proteins. The basic assumption is that homologs of interacting proteins have a high probability of being interaction partners as well. These homology-derived potential interactors are then called interologs.

This class is not instantiatable.

Some ideas are adapted from

Yu, H.; Luscombe, N. M.; Lu, H. X.; Zhu, X.; Xia, Y.; Han, J. J.; Bertin, N.; Chung, S.; Vidal, M. & Gerstein, M.
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.
Genome Res, 2004, 14, 1107-1118
Pubmed: 15173116

Author:
Jan Krumsiek

Method Summary
static ProteinNetwork calculateInterologs(ProteinNetwork toTransfer, ProteinNetwork mapping, InterologScorer scorer)
          Calculates interologs of an interaction network using a given protein mapping (which should contain homology information like bidirectional best hits).
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

calculateInterologs

public static ProteinNetwork calculateInterologs(ProteinNetwork toTransfer,
                                                 ProteinNetwork mapping,
                                                 InterologScorer scorer)
Calculates interologs of an interaction network using a given protein mapping (which should contain homology information like bidirectional best hits).

The resulting network will have the directedness of the original interaction network.

The mapping network can be a directed network but will be used in an undirected manner.

Parameters:
toTransfer - interaction network for which interologs will be calculated
mapping - the protein mapping to be used, can be BBHs for instance
scorer - scorer for the interolog edges or null to let all transferred edges have a weight of 1.0
Returns:
the transferred interolog network