NOTE: This was one of the original projects when we first got access to UK Biobank and was mainly intended to be used as a demo for other researchers. Since then, most of the templating and instructions have moved into the ukbAid package (https://github.com/steno-aarhus/ukbAid). Hence why this is archived.

mesh: The metabolic pathways between components of stature and HbA1c: An exploratory cross-sectional analysis in the UK Biobank

Shorter relative adult leg length (LL), a marker of adverse growth conditions during early childhood, is associated with a higher risk for type 2 diabetes. How this link is mediated metabolically is not well known in humans. Our aim was to explore how the components of stature influence the metabolic profile in adults and the consequent risk for type 2 diabetes through higher HbA1c.

Further project details can be found in the doc/protocol.Rmd file. However, here are some brief details:

• Population: Those without diabetes and who have had their stature measured in the UK Biobank.

• Exposures: Height, sitting height, and leg length.

• Comparisons: The exposure measures are used as continuous variables, so comparisons will be done on a continuum of increasing/decreasing exposure.

• Outcome: HbA1c

Explanation of workflow

This part of the README details how this research directory is structured, how files should be run, and what the different files do. The layout and setup of this project was designed for using RStudio and devtools. It is set up this way to make it easy for others to run the code and analyses for themselves and to scaffold onto the devtools workflow (used for R package development). For more detail on using this project workflow, see prodigenr.

Installing project R package dependencies

If dependencies have been managed by using usethis::use_package("packagename") through the DESCRIPTION file, installing dependencies is as easy as opening the mesh.Rproj file and running this command in the console:

# Might need to re-set these if `restore()` complains about PAT.
# gitcreds::gitcreds_set()
# credentials::set_github_pat(TRUE)
# Or more directly (readline to paste token in):
# Sys.setenv(GITHUB_PAT = readline())
renv::restore()
targets::tar_make()

Brief description of folder and file contents

The following folders contain:

• data/: Will contain the UK Biobank data (not saved to Git) as well as the intermediate results output files.

• data-raw/: Contains the R script to download the data, as well as the CSV files that contain the project variables and the variable list as named in the RAP.

• doc/: This file contains the R Markdown, Word, or other types of documents with written content, like the manuscript and protocol.

• R/: Contains the R scripts and functions to create the figures, tables, and results for the project.

• renv/: Contains the files needed by the renv package to help with installing the correct packages necessary for this project.

These files are for:

• .gitignore tells Git to ignore certain files from being tracked and prevents them from entering the version control history.
• .Rbuildignore tells devtools which files to not include when running functions such as devtools::load_all().
• DESCRIPTION is a standard file that includes metadata about your project, in a machine readable format for others to obtain information on about your project. It provides a description of what the project does and most importantly what R packages your project uses on.
• The .Rproj file dictates that the directory is a RStudio project. Open the project by opening this file.

All subsequent folders have their own README inside. See them for more details.