ParRADMeth

ParRADMeth, Parallel Regression Analysis of Differential Methilation is a parallel algorithm for the identification of differentially methylated regions in genomic analyses. Based on RADMeth, from The Smith Lab.

Prerequisites

Before starting the installation, please confirm that the following software is available in your system. Particular versions using during development are shown.

• GCC v8.3.0
• GSL v2.6
• make v3.82
• MPI compiler with support for OpenMP:
  • OpenMPI v3.1.4
• Git (Optional)

Different versions of the software may work but they have not been tested.

Compilation

The project was design so a system level instalation is not needed, but user level compilation and execution can be done. Compilation of the tool for your system architecture can be done by following these steps:

1. Download. First, obtain project files by cloning this git repository.
2. Compilation. In this step go to the root folder of the project and use make.
3. Instalation. In this steps, still on the root folder, use make install. This will place the executable on the bin/ folder.
4. Cleaning (Optional). Optionally, still on the root folder, use make clean to delete files generated during tool's compilation. Only unnecessary files are deleted, so executable files generated still work.

Execution

ParRADMeth must be executed with MPI execution commands (mpiexec (standard) or mpirun).Therefore, the tool can be executed using the following command from the root folder of the proyect:

mpiexec -n <numProcs> ./bin/ParRADMeth regression <options> <design_matrix> <proportion_table>

when numProcs is the number of MPI processes to execute, and options is a list of the following arguments:

• -h (Optional). Print usage and exit.
• -v (Optional). Verbose, print more run information.
• -factor <f> (Compulsory). The factor to test.
• -o (Optional). Output option.
• design_matrix (Compulsory). Path to the file containing the design matrix.
• proportion_table (Compulsory). Path to the file containing the proportion table.

License

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.