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.
Download zip-file or open the terminal and clone the repository:
cd ~ # go to folder
git clone https://github.com/UMCUGenetics/dIEM.git
|─── data (libraries for the dIEM algorithm)
|─── stofgroups (metabolite lists for the violin plots)
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.
- files listed under Folder Structure
- config.R
- excel output file from the inhouse DIMS pipeline with Z-scores
- 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