procope.evaluation.networkperformance
Class ComplexEnrichment

java.lang.Object
  extended by procope.evaluation.networkperformance.ComplexEnrichment

public class ComplexEnrichment
extends Object

Contains one static method to calculate the complex enrichment score of a network with respect to a complex set.

Author:
Jan Krumsiek

Constructor Summary
ComplexEnrichment()
           
 
Method Summary
static float calculateComplexEnrichment(ProteinNetwork network, ComplexSet reference, int numrand, boolean useWeightedScores)
          Calculates the complex enrichment of a given network with respect to a given complex set.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ComplexEnrichment

public ComplexEnrichment()
Method Detail

calculateComplexEnrichment

public static float calculateComplexEnrichment(ProteinNetwork network,
                                               ComplexSet reference,
                                               int numrand,
                                               boolean useWeightedScores)
Calculates the complex enrichment of a given network with respect to a given complex set. The complex enrichment score is the quotient of the average complex score of the reference complex set and a randomized copy of that reference set. The higher this value the more high-scoring edges the network contains within the complexes. Note that multiple calls of this function will cause slighty different results.

Parameters:
network - the network for which to calculate to complex enrichment
reference - reference complex set
numrand - number of randomizations, the average of all runs will be taken; this parameter is used to minimize variation in the results
useWeightedScores - calculate weighted complex set average score?
Returns:
the complex enrichment of that score with respect to the given complex set or 0 if no inner-complex edge has a nonzero value