Package edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal

Class RevealSearch

java.lang.Object

edu.cmu.tetrad.study.gene.tetrad.gene.algorithm.reveal.RevealSearch

public class RevealSearch
extends Object

This class contains as a member variable (cases) the time series data stored in an int array of microarray measurements. The values are assumed to have been binarized. The columns of the array correspond to genes and the rows correspond to times. The class contains methods for conducting searches for causal links where a genes expression is regulated by a set of parent genes. The search method calls the methods for computing entropies and measures of mutual information implemented in the RevealEvaluator class. This approach is described by Liang et al.

Author:

Frank Wimberly

Constructor Summary

Constructors

Constructor	Description
RevealSearch(int[][] cases, String[] names)

Method Summary

Modifier and Type	Method	Description
void	exhaustiveSearch(int lag)	This method computes m/e values for all single regulators, pairs and triples at a given time lag.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

RevealSearch

public RevealSearch(int[][] cases,
 String[] names)

Method Details

exhaustiveSearch

public void exhaustiveSearch(int lag)

This method computes m/e values for all single regulators, pairs and triples at a given time lag. The m/e value is the ratio of the mutual information between the regulated gene and the regulator set divided by the entropy of the regulated gene.