Data Processing for Fast-GC PTR-ToF-MS Analysis

This repository contains scripts to process GC-MS data for yeast fermentation studies. The analysis involves extraction of specific peaks from the spectral data for compounds of interest.

Scripts and Functions

Main Script

The main script (main.R) reads a dataset and calls functions from functions.R to perform data processing and peak detection. The main operations include:

• Reading data
• Setting global variables such as yeast_ids, compound_ids, times, replicates and mzs (m/z values of interest)
• Calling the function get_all_peaks() that performs data filtering, smoothing, peak detection, and data frame preparation for all combination of yeast, compound, time, and replicates specified by the global variables.

Functions

functions.R includes the following functions:

• filter_data(): filters the input data for specified parameters (yeast_id, compound_id, time_point, replicate)
• prepare_dataframe(): prepares a data frame with the peaks' information for a specific sample
• find_highest_peaks(): detects the highest peaks in the smoothed spectrum for a specific sample
• moving_average(): calculates the moving average for the input vector
• plot_spectrum_yeast(): creates a plot of the smoothed spectrum and saves it as a PDF
• get_all_peaks(): carries out data processing and peak detection for all combinations of yeast, compound, time, and replicates.

Usage

To use the script and functions, follow these steps:

1. Clone this repository to your local machine.
2. Navigate to the directory containing the repository via your R environment.
3. Make sure you have the necessary libraries installed (writexl, ggplot2, dplyr, pracma). If not, install them using the install.packages() function.
4. Open the main script and set the working directory to the location where your input data file (processedData4.csv) resides.
5. Adjust the global variables (yeast_ids, compound_ids, times, replicates and mzs) as needed.
6. Run the script. The function get_all_peaks() will process the data and extract the peaks for the conditions specified by the global variables.

If you want to generate plots for each condition, set the plot_data parameter in get_all_peaks() to TRUE.

Output

The get_all_peaks() function returns a data frame containing the peaks detected for each combination of yeast, compound, time, and replicates. If plot_data is set to TRUE, it will also generate a PDF plot for each condition and save it to your working directory.

License

This project is licensed under the MIT License.

Contact

If you have any questions or encounter any issues, please open an issue in this repository.

Author

Jan Effenberger 2023