Schweickart et al., "Metabolomic signatures of hypocaloric dietary interventions associate with breast cancer risk in the Nurses’ Health Study II", unpublished.
| File | Description |
|---|---|
internal_functions.R |
Helper functions (e.g. regression utilities) used in other scripts |
01_Preprocess_Controlled_Trials_data.R |
Harmonizes and preprocesses data from MSK & OSU controlled trials |
02_get_differential_metabolites.R |
Identifies diet-dependent differential metabolites |
03_Preprocess_NHS_data.R |
Preprocesses the NHSII data |
04_load_save_data.R |
Calculates diet scores and merges with NHSII metadata |
05_run_mwas.R |
Performs metabolite–breast cancer risk MWAS |
06_calculate_metabolite_concordance.R |
Computes concordance of metabolite effects |
Schweickart_2025_Tables.Rmd |
Generates summary tables from processed data |
Schweickart_2025_Figures.Rmd |
Produces Figures 2-4. |
To knit the R Markdown files:
rmarkdown::render("Schweickart_2025_Tables.Rmd")rmarkdown::render("Schweickart_2025_Figures.Rmd")
This code was created with R version 4.2.0 and Rstudio Version 2023.06.2+561 and tested on macOS (Sonoma 14.2.1) with a 2.3 GHz Quad-Core Intel Core i5 CPU.
The following R packages are required to run the above scripts:
- maplet (1.1.2)
- glue (1.8.0)
- dplyr (1.1.4)
- ggplot2 (4.0.2)
- tidyverse (2.0.0)
- openxlsx (4.2.8)
- purrr (1.0.2)
- cowplot (1.2.0)
- viridis (0.6.3)
- reshape (0.8.10)
- sva (3.46.0)
- gt (1.0.0)
- gtsummary (2.4.0)
- ggrepel (0.9.6)
- viridisLite (0.4.2)
- data.table (1.14.8)
- survival (3.8-3)
- lubridate (1.9.4)
- forcats (1.0.0)
- readr (2.1.5)
- tidyr (1.3.1)
- tibble (3.2.1)
- sas7bdat (0.8)
- chanmetab (0.1.14)
- ggpubr (0.6.1)
- caret (7.0-1)
- lattice (0.22-7)
- glmnet (4.1-10)
- Matrix (1.6-4)
- stringr (1.5.1)
- BiocParallel (1.32.6)
- genefilter (1.80.3)
- mgcv (1.9-3)
- nlme (3.1-168)
- readxl (1.4.5)
- SummarizedExperiment (1.28.0)
- Biobase (2.58.0)
- GenomicRanges (1.50.2)
- GenomeInfoDb (1.34.9)
- IRanges (2.32.0)
- S4Vectors (0.36.2)
- BiocGenerics (0.44.0)
- MatrixGenerics (1.10.0)
This repository does not contain the input data files for these scripts. Contact https://nurseshealthstudy.org/contact for NHSII data, and the corresponding authors for OSU and MSK data.