README.md

This repository is dedicated to the analysis undergone by Max Bladen between August and October (2023) for Patrick Albertus and Donald Lynch from the University of Cincinnati. The mixOmcis package was used in order to evaluate the efficacy of model building on lipid and proteomic data from high- and low- CAD risk diabetes patients. The repository is structued as follows:

• Config:
  • Contains a single .R file which handles the configuration of the .Rmd knitting process. Not relevant to actual analysis, purely to maintain consistency across reports
• Markdowns:
  • Series of .Rmd files, each corresponding to a single report file. All code can be found within these files. All analysis and figures should be reproducible by knitting these documents,
  • Note: some of these .Rmd files yield .rds files which downstream markdowns are dependent on.
• RDS:
  • Contains any .rds objects yielded and/or used by the .Rmd files in Markdowns. Subsequent analysis can be completed on these .rds objects
• Reports:
  • .html files yielded by knitting the .Rmd files in Markdowns. Best to download/clone this repository and view these .html files locally, as Github cannot render them properly
• Scripts:
  • Contains any .R files used as part of the analysis that are outside the .Rmd. Currently only contains Functions.R which is a sourced script used to store some custom functions which were repeatedly used.

To rerun the .Rmd scripts, make sure you adjust the wd variable in the Config/global_options.R script