Chemicals sets can be defined in many ways, enabling biological interpretation in different contexts. For example, a chemical ontology might be helpful in finding a group of structurally similar compounds that have the same origin. A pathway map shows the biochemical reactions and their regulations that transform a substrate into a product. A pharmacological action group may indicate function properties such as vitamins or pain-killers. A taxonomy set shows if compounds are coming from a specific microbial/plant genus. Overall, the more we analyze metabolomics data with different set definitions, more biological insights we might gain from it. Using these set definitions with ChemRICH is a simple exercise as an user does not need to obtain any database identifiers or have information about the precise structure of an annotated compound. We know how tedious and frustrating it is to get PubChem ID for lipid species !
You can follow this test case to get an idea how ChemRICH can be used for a set-definition. All you have to do is to change the 'set' column in the example excel file and update the ChemRICH results.
Download the example file . It is a metabolomics dataset with pathways as set definitions.
Save the example file in a new folder somewhere in your computer. Then in the RStudio, you need to set the new folder as a working directory (LINK).
Once you are in the working directory, copy and paste these three lines of R code in the R studio software.
run_chemrich_basic(inputfile = "chemrich_input_minimum.xlsx")
The output files are :
chemrich_class_impact_plot.png (PNG image of the chemrich impact plot)
chemrich_class_impact_plot.pptx (Power point of the ChemRICH impact plot)
chemRICH_class_results.xlsx ( Result Tables of the ChemRICH analysis)
chemrich_interactive.html (an interactive web-page to interact with the impact plot)
Hopefully, you were able to run it and get the results.
Modify the "set" and "order" columns in the input file and you can run ChemRICH for any type of set definitions. In future, we will be providing a range of set definitions for metabolites that can be used the the ChemRICH approach.