org.gersteinlab.regulation
Class DeletionProfile

java.lang.Object
  extended by org.gersteinlab.regulation.DeletionProfile

public class DeletionProfile
extends java.lang.Object

        A class for storing the deletion profile of all genes read from a file.
        

Version:
1.0 (August 20, 2008)
        Change History:
        1.0     - Initial version
        
Author:
Kevin Yuk-Lap Yip

Field Summary
protected  double eMean
           
protected  double eSD
           
protected  int geneCount
           
protected  java.lang.String[] geneNames
           
protected  double[][] profile
           
protected  double[] vMeans
           
 
Constructor Summary
DeletionProfile()
           
 
Method Summary
protected  void computeStats()
          1.
 double[][] getReactionProbs()
           
static DeletionProfile readProfile(java.io.Reader r)
          Read and return the profile in a file.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

geneCount

protected int geneCount

geneNames

protected java.lang.String[] geneNames

profile

protected double[][] profile

eMean

protected double eMean

eSD

protected double eSD

vMeans

protected double[] vMeans
Constructor Detail

DeletionProfile

public DeletionProfile()
Method Detail

readProfile

public static DeletionProfile readProfile(java.io.Reader r)
                                   throws java.io.IOException
Read and return the profile in a file.

Parameters:
r - The reader of the file
Returns:
The profile
Throws:
java.io.IOException

computeStats

protected void computeStats()
1. Initialize the mean of each gene by its wild type value 2. Identify points not affected by the deletions 3. Estimate mean and sd of global random error 4. Use the global random error to re-estimate mean of each gene 5. Repeat 2-4


getReactionProbs

public double[][] getReactionProbs()