ChemRICH for Multiple Conditions

Often, more than one groups are compared or more than one regression models are computed using metabolomics datasets. For this situation, you will need to create one input file having all pvalue and effect_size for each model/comparison, and then use a batch ChemRICH script to generate the set analysis results.

This example is from the KOMP metabolomics paper (LINK). We are using just three conditions to demonstrate the code. Input data can be found here (LINK). It does need SMILES codes and the class information for each identified metabolite. You can use the "Predict MeSH Classes" function to generate the class info for your list of compounds.

Download the input data file into a new folder. Then run the below R-code.

Instructions

source('https://raw.githubusercontent.com/barupal/ChemRICH/master/chemrich_multiple_groups.R ', echo=TRUE)

load.ChemRICH.Packages()

project_name <- "chemrich_1" # Provide this analysis a name. This will be prefixed to all the exported files.

classVariable <- "Class"

inputfile <- "20181015_KOMP_chemrich_input.xlsx"

chemrich_multi_group(inputfile)

# To generate a heatmap from the results of multiple comparisons, use the below code. Credit : https://github.com/chrisbrydges

source("https://raw.githubusercontent.com/chrisbrydges/chemRICH_heatmap/main/ChemRICH_heatmap.R")

chemrich_heatmap(input = "chemrich_results.xlsx")

Results of this analysis can be found here (LINK) and images (below).