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4. Tutorial
Note: PECA-core and PECA-N uses the same binary and Python script in the peca_core folder, PECA-R and PECA-pS uses the same set of binary and Python script in peca_r folder. All files in examples are in Unix format, please use unix2dos if you are on Windows platform.
Once the input parameter file and the two input files are prepared, you can run the PECA analysis using the following command:
> [path_to_peca_core]/peca_core_bin <input_parameter_filename_here>
The above step may take a long time (e.g. 1 hour). Hence do not log off your computer. If you are using linux platform, you can launch the command in screen interface while you are offline.
After the completion of the MCMC, run the Python script peca_core.py to get the summary and gene-specific plots
> python3 [path_to_peca_core]/peca_core.py
The output files are described in the Analysis Output section.
Following this step, a GSA analysis can be done on the change points scores. First the input parameter file:
Once the input parameter file is prepared, you can run the PECA GSA analysis using the following command:
> [path_to_peca_gsa]/gsa_bin <input_parameter_filename_here>
Once the input parameter file and the two input files are prepared, you can run the PECA analysis using the following command:
> [path_to_peca_R]/peca_r_bin <input_parameter_filename_here>
After the completion of the MCMC, run the Python script peca_r.py to get the summary and gene-specific plots
> python3 [path_to_peca_R]/peca_r.py
Once the input parameter file and the two input files are prepared, you can run the PECA analysis using the following command:
> [path_to_peca_R]/peca_r_bin <input_parameter_filename_here>
After the completion of the MCMC, run the Python script peca_r.py to get the summary and gene-specific plots
> python3 [path_to_peca_R]/peca_r.py
For mRNA-level analysis, you can place the mRNA data as FILE_Y, and leave FILE_X empty.
Once the input parameter file and the two input files are prepared, you can run the PECA analysis using the following command:
> [path_to_peca_core]/peca_core_bin <input_parameter_filename_here>
After the completion of the MCMC, run the Python script peca_core.py to get the summary and gene-specific plots
> python3 [path_to_peca_core]/peca_core.py