evaluation.networkperformance
Class ROC

java.lang.Object
  extended by evaluation.networkperformance.ROC

public class ROC
extends Object

Contains static methods to calculate ROC curves for protein networks. These ROC curves are a quality measure and describe how good the scores within the network fit to a given complex set.

Calculation procedure

ROC curves are computed as follows.

  1. As there are too many possible negative edges a negative set is sampled. To generate this set, edges between random proteins are choosen which are not within a complex and optionally not colocalized (which of requires course requires LocalizationData).
  2. Each edge in the network is assigned one of the following states:
  3. [text mit threshold runterziehen und so]

Author:
jan

Constructor Summary
ROC()
           
 
Method Summary
static List<ROCCurve> calculateROCCurves(List<ProteinNetwork> scoreNetworks, ComplexSet reference, ComplexSet referenceForNegativeSet, LocalizationData locData)
          Calculate the ROC curves for a given set of networks.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ROC

public ROC()
Method Detail

calculateROCCurves

public static List<ROCCurve> calculateROCCurves(List<ProteinNetwork> scoreNetworks,
                                                ComplexSet reference,
                                                ComplexSet referenceForNegativeSet,
                                                LocalizationData locData)
Calculate the ROC curves for a given set of networks. Can use a different complex set for the identification

Parameters:
scoreNetworks - list of networks for which the ROC curves will be calculated
reference - reference set to be used
referenceForNegativeSet - reference set
locData - localization data, use null if you do not want to use localization data for negative set generation
Returns:
list of ROC curves for the given networks