Waschina / chem_shift_imaging_NMR

chem_shift_imaging_NMR

This repository contains the point-wise binned NMR spectra as well as the data analysis R-code for the study "Chemical shift imaging by NMR metabolomics using in tube extraction and slice selection." by Silvio Waschina (Kiel University), Karsten Seeger (University of Lübeck).

Dependencies

• R (version >4.1.2)
• R-packages
  • data.table (v. 1.14.2)
  • speaq (v. 2.6.1)
  • ggplot2 (v. 3.3.5)
  • ggrepel (v. 0.9.1)
  • bit64 (v. 4.0.5)
  • egg (v. 0.4.5)
  • missForest (v. 1.4)
  • ica (v 1.0-3)

Repository structure

• directory analysis/v1/scripts/ - contains all R-scripts
• directory analysis/v1/plots/ - should be created if not already there. Plots in PDF format will be saved here.
• directory data/clean/ contains the sample meta information (e.g. coordinates of samples)
• directory data/raw/ contains the actual data (point-wise binned spectra). Files are gzipped plain text files.

Data analysis

The data analysis is performed using R. To re-run the analysis, simply run the following commands from a bash terminal within the project directory.

Bear-shaped ham

Rscript analysis/v1/baerchi_01.R

Bierschinken

Rscript analysis/v1/beerschi_01.R