dIEM with visualization

For untargeted metabolomics, this tool calculates probability scores for metabolic disorders. In addition, it provides visual support with violin plots of the mass spectrometry (DI-HRMS) measurements for the lab specialists.

Installation

Download zip-file or open the terminal and clone the repository:

cd ~ # go to folder
git clone https://github.com/UMCUGenetics/dIEM.git

Folder Structure

|─── data (libraries for the dIEM algorithm)
|─── stofgroups (metabolite lists for the violin plots)

Usage

The tool can be run in RStudio:

• Setting the working directory in the same directory as the config.R file.
• Running the packages_installation.R script.
• Editing the config.R file with the appropriate paths and variables.
• Running the main script: dIEM_violin_pipeline.R

If the main script makes RStudio crash, there is probably not enough RAM on your device.

Input

• files listed under Folder Structure
• config.R
• excel output file from the inhouse DIMS pipeline with Z-scores

Output

• violin plots overview pdf file (all patients with a Z-score higher than 5 are annotated)
• violin plots per patient, stofgroups pdf file
• output algorithm excel file (with probability scores per metabolic disease)
• input csv file for shiny app
• log file