This software is intended for creating the data matrices.

REQUIREMENTS
For the DNA-methylation matrix creator:
Java Runtime Environment 7 or upper version;
hadoop-1.2.1;
pig-0.13.0.

For the RNA-sequencing and combined matrix creator:
Java Runtime Environment 7 or upper version


INPUT
For the input please consider the TCGA2BED version of TCGA available at bioinf.iasi.cnr.it/tcga2bed.


DNA-METHYLATION MATRIX CREATOR
For creating the DNA-methylation data matrix open the terminal and run the following command:

$ java -jar DNA-Methylation_MatrixCreator.jar output_path disease_name input_path

where 
output_path, is a path of a folder in your file system where you want to create the final matrix;
disease_name, is the name of the tumor or disease (or a code) for identifying the final matrix file;
input_path, is the path of the folder where the bed files are located. 

example: java -jar DNA-Methylation_MatrixCreator.jar output_DNAMeth_matrix BreastCancer brca/dnamethylation450


RNA-SEQUENCING MATRIX CREATOR
For creating the RNA-sequencing data matrix open the terminal and run the following command:

$ java -jar RNA-sequencing_MatrixCreator.jar output_path disease_name path_input

where 
output_path, is a path of a folder in your file system where you want to create the final matrix;
disease_name, is the name of the tumor or disease (or a code) for identifying the final matrix file;
input_path, is the path of the folder where the bed files are located.

example: java -jar RNA-sequencing_MatrixCreator.jar output_RNASeq_matrix BreastCancer brca/gene.quantification


COMBINED MATRIX CREATOR
For creating the combined data matrix open the terminal and run the following command:

$ java -jar Combined_MatrixCreator.jar output_path disease_name dnaMethylatin_matrix_path rnaSequencing_matrix_path

where 
output_path, is a path of a folder in your file system where you want to create the final matrix;
disease_name, is the name of the tumor or disease (or a code) for identifying the final matrix file;
dnaMethylatin_matrix_path, is the path where the DNA-methylation matrix is located;
rnaSequencing_matrix_path, is the path where the RNA-sequencing matrix is located.

example: java -jar Combined_MatrixCreator.jar output_INT_matrix BreastCancer output_DNAMeth_matrix/DNA-methylation_Matrix_BreastCancer.csv output_RNASeq_matrix/RNA-sequencing_Matrix_BreastCancer.csv


CONTACTS
Please contact Eleonora Cappelli (eleonora.cappelli@uniroma3.it) if you have questions.