* * For running the main (i.e. the runnable jar), the format of the input should be (in this order): * 1. A gene expression matrix file. This is a tab delimited file in which the first row * contains the condition names, and the first column contains the gene names. * For example, see the LungCancer.txt file LungCancer.zip. * 2. A "classes file". This file contains partitioning of the conditions in the matrix to groups. * We assume that conditions from the same groups are adjacent in the matrix. * This file is tab delimited, in each row there are three columns: the start index of the * current group (enumeration of the conditions starts from zero),the end index, and the group name. * For example, see the classesFile.txt in LungCancer.zip * 3. A number between 0 and the number of classes -1 that specifies the class of interest. * 4. A name of an output file. * * OPTIONAL: 5. out=1 if you want to print the DC and CG graphs (as matrices). * 6. K=value to change the default K value (currently, default is 2). * * All output files prefixes are the name of the output path specified by the user. * It creates the following files, according to the suffixes: * 1. _Modules.txt - a flat file with the gene to modules assignments. * in this file, up or down specifies from which DICER analysis the modules where detected. * 2. _metaGraph.sif - a SIF file that represents the DC map among the modules * 3. _metaGraph.txt - a file with the edge scores for _metaGraph.sif * 4. The final output file is the output path indicated by the user and it contains * all gene to meta-module or DC cluster mappings. * */