Lipidomics Data Post-Processing in R

CDM5104 Project Work

Summary

In this project, you will go through some steps of a lipidomics data processing workflow using R with tidyverse packages. The example dataset used in the project was obtained from Tan et al. 'Variability of the Plasma Lipidome and Subclinical Coronary Atherosclerosis' DOI: 10.1161/atvbaha.121.316847

You will inspect and process this targeted mass spectrometry (MS)-based plasma lipidomics raw dataset, starting from peak areas, moving to data quality control and ending with a table of QC-filtered lipid concentration values.

2. Installing R and RStudio

If you have these programs already installed on your computer, please ensure that you have R Version 4.1 or higher, and RStudio Version 2022.02 or higher installed. Otherwise, or if you have not yet installed them, proceed with following sequence:

1. R: Download from https://cloud.r-project.org{.uri}

2. RStudio: download from https://posit.co/download/rstudio-desktop{.uri}

3. Installing R packages

Please install following packages by running following code in your R console:

# CRAN packages
install.packages(c("here", "tidyverse", "broom", "ggrepel", "ggpmisc"))

# Bioconductor packages
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") 
  BiocManager::install(c("rgoslin"))

4. Download and run the RStudio project

Download the R Project containing the scripts and data used for project work from this repository (click on the green button "<>Code" and then "Download ZIP"). Alternatively, you can clone this repository using RStudio or Git. Do not hesitate to contact us if you have any questions. Double-click the <CDM5104_Lipidomics.Rproj> file to open the project in RStudio. (Do not just open the CDM5104_Project.qmd file)

5. Author

• Bo Burla - Singapore Lipidomics Incubator @ NUS

6. Acknowledgments

• Authors of the dataset used in this project work: Tan et al., Atheroscler Thromb Vasc Biol, 2021 DOI: 10.1161/atvbaha.121.316847
• Members of the Singapore Lipidomics Incubator

License

This project is licensed under the MIT License - see the LICENSE.md file for details