|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectevaluation.complexquality.Colocalization
public class Colocalization
Implements measures for the degree of colocalization of proteins contained in a predicted protein complex.
Two scoring methods are implemented, one of them (colocalization score) is part of our own work, the second method (PPV) was proposed in
Pu et al.
Identifying functional modules in the physical interactome of Saccharomyces cerevisiae.
Proteomics, 2007, 7, 944-960
For detailed information about how both types of scores are calculated please consult the online manual of this library.
Constructor Summary | |
---|---|
Colocalization(LocalizationData data)
Creates a new colocalization score calculator. |
Method Summary | |
---|---|
float |
getAverageColocalizationScore(ComplexSet complexes,
boolean weighted,
boolean ignoreMissing)
Calculates the average colocalization score for a given complex set. |
float |
getAveragePPV(ComplexSet complexes,
boolean weighted,
boolean ignoreMissing)
Calculates the average PPV for a given complex set. |
float |
getColocalizationScore(Complex complex)
Calculates the colocalization score of a given complex. |
float |
getPPV(Complex complex)
Calculates the PPV according to TODO: [b] et al, 200x |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public Colocalization(LocalizationData data)
data
- localization data to be usedMethod Detail |
---|
public float getPPV(Complex complex)
complex
- for which the PPV will be calculated
public float getColocalizationScore(Complex complex)
complex
- complex for which the score will be calculated
public float getAverageColocalizationScore(ComplexSet complexes, boolean weighted, boolean ignoreMissing)
complexes
- complex set for which the average score will be calculatedweighted
- calculate sum weighted by the complex sizes?ignoreMissing
- ignore cases where there are no localization data
for any protein in a complex (colocalization score == 0)?
public float getAveragePPV(ComplexSet complexes, boolean weighted, boolean ignoreMissing)
complexes
- complex set for which the average PPV will be calculatedweighted
- calculate sum weighted by the complex sizes?ignoreMissing
- ignore cases where there are no localization data
for any protein in a complex (colocalization score == 0)?
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |