scripts
Class GenerateWeightedGraphForCytoscape

java.lang.Object
  scripts.GenerateWeightedGraphForCytoscape

public class GenerateWeightedGraphForCytoscape
extends java.lang.Object

This script is for creating sif files for analysis in cytoscape. The input is an expression matrix, a list of genes of interest, output path name, minimum correlation value, classes file, and the class of interest index. The output is as follows: create a sif file. A node is a gene from the input list. An edge is a gene pair with correlation > min_value. The correlation is calculated in the window of the selected class. These windows (i.e., sample to class mapping) is given in the classes file.

Constructor Summary

GenerateWeightedGraphForCytoscape()

Method Summary

static void

main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Constructor Detail

GenerateWeightedGraphForCytoscape

public GenerateWeightedGraphForCytoscape()

Method Detail

main

public static void main(java.lang.String[] args)

Parameters:

args -