Plasma and Platelet Lipidome Changes in Fabry Disease

Bo Burla, Jeongah Oh, Albina Nowak, Nathalie Piraud, Eduardo Meyer, Ding Mei, Anne K Bendt, Jan-Dirk Studt, Beat M Frey, Federico Torta, Markus R Wenk, and Pierre-Alexandre Krayenbuehl

Affiliations of main authors: Singapore Lipidomics Incubator, Life Sciences Institute; Department of Biochemistry Yong Loo Lin School of Medicine; National University of Singapore

2024

Summary

This repository contains the R used to process and QC filter the raw data (peak areas), and for the data analysis and generating of figures and tables

Getting the Code

All R code and datasets are provided as an RStudio project. The easiest way run this code is to clone the repository within RStudio (https://github.com/SLINGhub/Burla_2024_FabryLipidomics.git). Alternatively, you can also download the Github Repository and open the Rstudio project.

Setting up the Code

By default, the dependencies for this project are managed using renv to improve reproducibility and facilitate installation of required packages. After cloning, the required packages can be automatically installed by running following command in the console:

renv::restore()

Should you prefer to use your local R library instead, you can turn renv off by running following command:

renv::deactivate() 

Directory Structure

• analysis Quarto notebooks with data processing and analysis workflows
• data/
  • LipidomicsAnalyses/ Peak area files (*.CSV in subfolder MH) and analysis metadata ( *.XLSM)
  • processed/ Processed data (concentrations, QC filtered), output of 01_data-preprocessing.qmd
  • StudyMetadata/ Subject metadata and clinical laboratory analysis values
• output/ Generated figures and tables
• R/ R scripts with functions for plotting and managing of lipid names
• renv/ Used by renv

Running the Analysis

• Open the folder analysis
• To process the raw data run all chunks in 01_data-preprocessing.qmd
• To generate figures and tables run all chunks in 02_manuscript-figures-tables.qmd

Releases

v1.0.0: First submitted version

Contact

• Code and Data Analysis: Bo Burla (lsibjb@nus.edu.sg{.email})
• Manuscript: Bo Burla (lsibjb@nus.edu.sg{.email}) and Pierre-Alexandre Krayenbuhl (pierrea.krayenbuehl@usz.ch{.email})

License

The code in this analysis is covered by the MIT license

sessionInfo

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.0

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Singapore
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] patchwork_1.1.3  ggpubr_0.6.0     ggrepel_0.9.3    ggsignif_0.6.4   gt_0.9.0         rlang_1.1.1      glue_1.6.2       ggpattern_1.0.1  lubridate_1.9.3  forcats_1.0.0    stringr_1.5.0    dplyr_1.1.3     
[13] purrr_1.0.2      readr_2.1.4      tidyr_1.3.0      tibble_3.2.1     tidyverse_2.0.0  here_1.0.1       midar_0.1.1.9001 ggplot2_3.4.3   

loaded via a namespace (and not attached):
 [1] polynom_1.4-1         readxl_1.4.3          magrittr_2.0.3        clue_0.3-65           GetoptLong_1.0.5      matrixStats_1.0.0     compiler_4.3.1        mgcv_1.9-0            systemfonts_1.0.4    
[10] png_0.1-8             vctrs_0.6.3           quantreg_5.97         pkgconfig_2.0.3       shape_1.4.6           crayon_1.5.2          fastmap_1.1.1         backports_1.4.1       labeling_0.4.3       
[19] utf8_1.2.3            tzdb_0.4.0            ragg_1.2.5            MatrixModels_0.5-2    bit_4.0.5             xfun_0.40             broom_1.0.5           parallel_4.3.1        cluster_2.1.4        
[28] R6_2.5.1              stringi_1.7.12        RColorBrewer_1.1-3    car_3.1-2             cellranger_1.1.0      Rcpp_1.0.11           iterators_1.0.14      knitr_1.44            usethis_2.2.2        
[37] IRanges_2.34.1        Matrix_1.6-1.1        splines_4.3.1         timechange_0.2.0      tidyselect_1.2.0      abind_1.4-5           rstudioapi_0.15.0     yaml_2.3.7            doParallel_1.0.17    
[46] codetools_0.2-19      lattice_0.21-9        withr_2.5.1           survival_3.5-7        ggpp_0.5.4            zip_2.3.0             xml2_1.3.5            circlize_0.4.15       pillar_1.9.0         
[55] BiocManager_1.30.22   carData_3.0-5         renv_1.0.3            foreach_1.5.2         stats4_4.3.1          generics_0.1.3        vroom_1.6.4           rprojroot_2.0.3       S4Vectors_0.38.2     
[64] hms_1.1.3             munsell_0.5.0         scales_1.2.1          tools_4.3.1           ggpmisc_0.5.4-1       SparseM_1.81          openxlsx_4.2.5.2      fs_1.6.3              grid_4.3.1           
[73] colorspace_2.1-0      nlme_3.1-163          cli_3.6.1             textshaping_0.3.6     fansi_1.0.4           ComplexHeatmap_2.16.0 gtable_0.3.4          ggh4x_0.2.6           rstatix_0.7.2        
[82] digest_0.6.33         BiocGenerics_0.46.0   rjson_0.2.21          farver_2.1.1          htmltools_0.5.6       lifecycle_1.0.3       GlobalOptions_0.1.2   bit64_4.0.5           MASS_7.3-60