scripts
Class GetMetaGraphFromSol

java.lang.Object
  scripts.GetMetaGraphFromSol

public class GetMetaGraphFromSol
extends java.lang.Object

This script calculates the "meta-file" of a clustering solution. It was used, for example, to create the map of DC between modules. This analysis gives an overview map of the DC instead of analyzing specific gene pairs. To use this script, you first need to save the graphs calculated by DICER. This is done by giving an additional parameter to DICER (see the instructions in DIECER_main). The input is: the expression matrix, the path in which the DICER graphs are kept, a clustering solution (i.e., gene to gene sets mapping). For DICER analysis we recommend using the modules file as we are interested here in a meta-graph of these modules. Also, you can add an optinal input: gene to pathway mapping and FDR threshold. When this input is given, we also output the enrichment analysis results. In the meta-graph we add an edge between tow modules in the sum of LLR scores between these modules in > 0. Also, in the sif file we keep the "edge type". That is, if the edge denotes down correlation or up-correlation.

Constructor Summary

GetMetaGraphFromSol()

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

GetMetaGraphFromSol

public GetMetaGraphFromSol()

Method Detail

main

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

Parameters:

args -