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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