procope.evaluation.comparison
Class ComplexSetComparison

java.lang.Object
  extended by procope.evaluation.comparison.ComplexSetComparison

public class ComplexSetComparison
extends Object

This class contains static methods for the comparison of two complex sets. The methods can be used to identify and investigate similarities and difference between two sets.

The class is not instantiatable.

Author:
Jan Krumsiek

Method Summary
static BroheeSimilarity broheeComparison(ComplexSet candidate, ComplexSet reference)
          Calculate complex set similarity after
static int complexesOverlap(Complex complex1, Complex complex2)
          Calculate the number of proteins which overlap between two given complexes.
static int[][] complexSetsOverlap(ComplexSet setA, ComplexSet setB)
          Calculates the overlap matrix for two given complex sets.
static ComplexMappings mapComplexes(ComplexSet setA, ComplexSet setB, int overlapThreshold)
          Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes.
static ComplexMappings mapComplexesConsistently(ComplexSet setA, ComplexSet setB, int overlapThreshold)
          Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes.
static ComplexMappings mapComplexesExactly(ComplexSet setA, ComplexSet setB)
          Find complexes in two given complex sets which are identical
static ComplexMappings mapComplexesMultiple(ComplexSet setA, ComplexSet setB, int overlapThreshold)
          Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

broheeComparison

public static BroheeSimilarity broheeComparison(ComplexSet candidate,
                                                ComplexSet reference)
Calculate complex set similarity after

Brohée, S. & van Helden, J.
Evaluation of clustering algorithms for protein-protein interaction networks.
BMC Bioinformatics, 2006, 7, 488
Pubmed: 17087821 For more information see: BroheeSimilarity

Parameters:
candidate - candidate complex set
reference - reference complex set
Returns:
similarity object for the two given complex sets

mapComplexesConsistently

public static ComplexMappings mapComplexesConsistently(ComplexSet setA,
                                                       ComplexSet setB,
                                                       int overlapThreshold)
Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes. This method only maps two complexes if both complexes do not have any other overlaps above the given threshold in the other set.

Parameters:
setA - first complex set
setB - second complex set
overlapThreshold - minimum overlap of proteins needed to map two complexes to each other (the literature often recommends a value of 2 here)
Returns:
list of mappings between the two complex sets

mapComplexesExactly

public static ComplexMappings mapComplexesExactly(ComplexSet setA,
                                                  ComplexSet setB)
Find complexes in two given complex sets which are identical

Parameters:
setA - first complex set
setB - second complex set
Returns:
list of mappings of identical complexes between the two complex sets

mapComplexes

public static ComplexMappings mapComplexes(ComplexSet setA,
                                           ComplexSet setB,
                                           int overlapThreshold)
Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes. This method only maps each complex of a set once. If there is more than one mapping candidate in the other set the one with the largest overlap will be used.

Parameters:
setA - first complex set
setB - second complex set
overlapThreshold - minimum overlap of proteins needed to map two complexes to each other (the literature often recommends a value of 2 here)
Returns:
list of mappings between the two complex sets

mapComplexesMultiple

public static ComplexMappings mapComplexesMultiple(ComplexSet setA,
                                                   ComplexSet setB,
                                                   int overlapThreshold)
Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes. This method calculates multiple mappings, i.e. the result will contain one mapping for each pair of complexes in the two sets whose overlap is above the given threshold.

Parameters:
setA - first complex set
setB - second complex set
overlapThreshold - minimum overlap of proteins needed to map two complexes to each other (the literature often recommends a value of 2 here)
Returns:
list of mappings between the two complex sets

complexesOverlap

public static int complexesOverlap(Complex complex1,
                                   Complex complex2)
Calculate the number of proteins which overlap between two given complexes.

Parameters:
complex1 - first complex
complex2 - second complex
Returns:
overlap between the two complexes

complexSetsOverlap

public static int[][] complexSetsOverlap(ComplexSet setA,
                                         ComplexSet setB)
Calculates the overlap matrix for two given complex sets. Each entry m(i,j) of the matrix contains the overlap between the i-th complex of the first set and the j-th complex of the second complex set.

Parameters:
setA - first complex set
setB - second complex set
Returns:
overlap matrix for the two given complex sets