procope.evaluation.complexquality
Class Colocalization

java.lang.Object
  extended by procope.evaluation.complexquality.Colocalization

public class Colocalization
extends Object

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.

Author:
Jan Krumsiek

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 Pu et al., 2007
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Colocalization

public Colocalization(LocalizationData data)
Creates a new colocalization score calculator.

Parameters:
data - localization data to be used
Method Detail

getPPV

public float getPPV(Complex complex)
Calculates the PPV according to Pu et al., 2007

Parameters:
complex - for which the PPV will be calculated
Returns:
colocalization PPV of that complex or 0 if not at least two proteins have localization data in the set

getColocalizationScore

public float getColocalizationScore(Complex complex)
Calculates the colocalization score of a given complex.

Parameters:
complex - complex for which the score will be calculated
Returns:
colocalization score of that complex or 0 if not at least two proteins have localization data in the set

getAverageColocalizationScore

public float getAverageColocalizationScore(ComplexSet complexes,
                                           boolean weighted,
                                           boolean ignoreMissing)
Calculates the average colocalization score for a given complex set.

Parameters:
complexes - complex set for which the average score will be calculated
weighted - 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)?
Returns:
average colocalization score for that complex set

getAveragePPV

public float getAveragePPV(ComplexSet complexes,
                           boolean weighted,
                           boolean ignoreMissing)
Calculates the average PPV for a given complex set.

Parameters:
complexes - complex set for which the average PPV will be calculated
weighted - 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)?
Returns:
average PPV for that complex set