fameR

A reproducible R pipeline for end‑to‑end processing of GC‑FID fatty acid methyl ester (FAME) datasets. This workflow automates cleaning, calibration, quantification, metadata integration, QC checks, and visualization producing tidy, analysis‑ready outputs with minimal manual intervention. This pipeline was built to keep all data processing steps clear, reproducible, and instrument‑agnostic, so the focus can stay on interpreting the biological data rather than spending time navigating GUI‑based data processing.

Key Features

• Automated import and cleaning of ChemStation (or other chromatography data acquisiton software) GC‑FID integration reports
• Calibration‑level mapping and extraction of slopes, intercepts, and R² values
• Quantification of calibrated and surrogate‑calibrated compounds
• Integration with experimental metadata
• Quality‑control checks for internal standard issues and abnormal FAME profiles
• Export of tidy datasets, calibration plots, and FAME‑profile visualizations
• Example dataset and metadata included for demonstration

Getting Started

1. Install Required Packages

Install required packages before running the pipeline:

• tidyverse
• readxl
• stringr
• ggpmisc
• openxlsx
• writexl
• ggpubr
• rstatix
• tools

2. Prepare Input Files

The pipeline expects:

• GC‑FID integration reports (Tidy XLSX format)
• Experiment metadata (Tidy XLSX format)
• FAME external standards calibration matrix
• Optional: surrogate quantification rules - this is important to quantify "novel" FAME - these are FAME that are present in the sample but not in the external standard mix

Example files are provided in data_example/.

3. Update User Inputs

In FAME_pipeline.Rmd, update the paths under the USER INPUT sections:

• GC‑FID data folder
• Calibration information file
• Quantification rules
• Metadata file
• Export directory

4. Run the Pipeline

Run the R Markdown document chunk‑by‑chunk paying attention to any warnings or knit the full workflow.

Generated outputs include:

• QC summaries and alerts
• Calibration curves (one JPEG per GC-FID run)
• GCFID_Results_Cleaned.xlsx (Total FAME/unit mass of dry sample & individual FAME% integrated to metadata)
• Boxplots of Total FAME/unit mass of dry sample (faceted by Experiment_ID)
• Boxplots of Individual FAME % composition (faceted by Experiment_ID)
• Kruskal-Wallis statistical tests results

Example Data

data_example/ includes:

• Synthetic GC‑FID integration reports
• Sample calibration matrix
• Example quantification rules
• Example metadata
• Expected outputs

Copyright/Publication/Citation

This open-source R pipeline was approved for public release by the Richard P. Feynman Center for Innovation (FCI) at Los Alamos National Laboratory (LANL) under LANL O-number: O5145.

If this pipeline contributes to your work, please cite Placeholder for publication.

© 2026. Triad National Security, LLC. All rights reserved. This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security Administration. All rights in the program are reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear Security Administration. The Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.