org.gersteinlab.regulation
Class DeletionProfile
java.lang.Object
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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
DeletionProfile
public DeletionProfile()
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()