Kegg

Annotating KEGG compounds to pathway

To annotate a list of KEGG compounds to the KEGG pathways where they are involved I used the R package KEGGREST from Bioconductor. library(KEGGREST) So, having a list of KEGG compounds saved in a character vector like kegg_compounds, we use the method keggGet in batches of maximum 10 compounds to annotate them. The following (rudimentary) code, queries the database in batches of ten compounds fiddling a list (pathways) where it creates an entry per pathway and updates the field compounds with the compounds from kegg_compounds for each pathway.