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java.lang.Objectevaluation.comparison.ComplexSetComparison
public class ComplexSetComparison
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.
Method Summary | |
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static BroheeSimilarity |
broheeComparison(ComplexSet candidate,
ComplexSet reference)
Calculate complex set similarity after Brohée, S. & van Helden, J. |
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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static BroheeSimilarity broheeComparison(ComplexSet candidate, ComplexSet reference)
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
candidate
- candidate complex setreference
- reference complex set
public static ComplexMappings mapComplexesConsistently(ComplexSet setA, ComplexSet setB, int overlapThreshold)
setA
- first complex setsetB
- second complex setoverlapThreshold
- minimum overlap of proteins needed to map two
complexes to each other (the literature often recommends a value
of 2 here)
public static ComplexMappings mapComplexesExactly(ComplexSet setA, ComplexSet setB)
setA
- first complex setsetB
- second complex set
public static ComplexMappings mapComplexes(ComplexSet setA, ComplexSet setB, int overlapThreshold)
setA
- first complex setsetB
- second complex setoverlapThreshold
- minimum overlap of proteins needed to map two
complexes to each other (the literature often recommends a value
of 2 here)
public static ComplexMappings mapComplexesMultiple(ComplexSet setA, ComplexSet setB, int overlapThreshold)
setA
- first complex setsetB
- second complex setoverlapThreshold
- minimum overlap of proteins needed to map two
complexes to each other (the literature often recommends a value
of 2 here)
public static int complexesOverlap(Complex complex1, Complex complex2)
complex1
- first complexcomplex2
- second complex
public static int[][] complexSetsOverlap(ComplexSet setA, ComplexSet setB)
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.
setA
- first complex setsetB
- second complex set
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