This software is intended for running the classification procedures.

CLASSIFICATION WITH C4.5
To execute the classification with the C4.5 algorithm open the terminal and run the following command:

$ java -jar J48.jar input_file_path output_file_name folds_number

where 
input_file_path, is a path of the matrix file in your file system that you want to process;
output_file_name, is the name of the output file;
folds_number, is the number of folds for cross validation sampling.

example: java -jar J48.jar input_DNAMeth_matrix/DNA-methylation_Matrix_BreastCancer.csv breastCancer_DNAMeth 10


CLASSIFICATION WITH RIPPER
To execute the classification with the RIPPER algorithm open the terminal and run the following command:

$ java -jar Jrip.jar input_file_path output_file_name folds_number

where 
input_file_path, is a path of the matrix file in your file system that you want to process;
output_file_name, is the name of the output file;
folds_number, is the number of folds for cross validation sampling.

example: java -jar Jrip.jar input_DNAMeth_matrix/DNA-methylation_Matrix_BreastCancer.csv breastCancer_DNAMeth 10

For big data matrices you can specify how much memory space you need for the execution, for example to allocate 6 GB of RAM:
java -Xmx6g -jar Jrip.jar input_DNAMeth_matrix/DNA-methylation_Matrix_BreastCancer.csv breastCancer_DNAMeth 10

CLASSIFICATION WITH Random Forest
To execute the classification with the RIPPER algorithm open the terminal and run the following command:

$ java -jar RandomForest.jar input_file_path output_file_name folds_number number_of_trees

where 
input_file_path, is a path of the matrix file in your file system that you want to process;
output_file_name, is the name of the output file;
folds_number, is the number of folds for cross validation sampling;
number_of_trees, is the number of the trees in the forest.

example: java -jar RandomForest.jar input_DNAMeth_matrix/DNA-methylation_Matrix_BreastCancer.csv breastCancer_DNAMeth 10 30

For big data matrices you can specify how much memory space you need for the execution, for example to allocate 6 GB of RAM:
java -Xmx6g -jar RandomForest.jar input_DNAMeth_matrix/DNA-methylation_Matrix_BreastCancer.csv breastCancer_DNAMeth 10 30


CLASSIFICATION WITH CAMUR
Please refer to http://dmb.iasi.cnr.it/camur.php for running the CAMUR classification tool.


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