methods.scores
Class PECalculator

java.lang.Object
  extended by methods.scores.PECalculator
All Implemented Interfaces:
ProteinSet, ScoresCalculator

public class PECalculator
extends Object
implements ScoresCalculator

Calculates Purification Enrichment scores according to

Collins et al.
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.
Mol Cell Proteomics, 2007, 6, 439-450

For more information about this scoring method please check out the online manual.

Author:
Jan Krumsiek

Constructor Summary
PECalculator(PurificationData data, float r, float pseudocount)
          Creates a new Purification Enrichment calculator.
 
Method Summary
 Set<Integer> getProteins()
          Returns all proteins of the purification data set used in this scores calculator
 float getScore(int protA, int protB)
          Calculates the Purification Enrichment score for two given proteins.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PECalculator

public PECalculator(PurificationData data,
                    float r,
                    float pseudocount)
Creates a new Purification Enrichment calculator.

Parameters:
data - purification data to be used
r - r parameter (see original literature)
pseudocount - pseudo-count (see original literature)
Method Detail

getScore

public float getScore(int protA,
                      int protB)
Calculates the Purification Enrichment score for two given proteins.

Specified by:
getScore in interface ScoresCalculator
Parameters:
protA - first protein
protB - second protein
Returns:
interaction score of the two proteins

getProteins

public Set<Integer> getProteins()
Returns all proteins of the purification data set used in this scores calculator

Specified by:
getProteins in interface ProteinSet
Specified by:
getProteins in interface ScoresCalculator
Returns:
a set of internal IDs