Hi all, I'm using clusterProfiler to check a list of genes for KEGG pathway enrichment.

While that list of genes did not show any significant enrichment (as was expected), I was still curious which pathways they mapped to.

To figure this out, I set pvalueCutoff=1 and qvalueCutoff=1 assuming that the result should then show me all pathways to which genes map. However, the analysis only returns a list of 6 pathways. Is there some additional filtering going on that I'm not aware of? (I have a list of ~450 E. coli genes that map to all sorts of KEGG pathways).

Here is the code I'm using:

# functions
KEGG_enrichments <- function(gene_list) {
  library(clusterProfiler)

  # KEGG pathway overrepresentation
  kk <- enrichKEGG(gene = gene_list,
                 organism = 'eco',
                 pvalueCutoff = 1,
                qvalueCutoff = 1,)



  return(kk)
}

# call functions
KEGG_enrichment = KEGG_enrichments(a_gene_list)
head(KEGG_enrichment)

Thanks a lot for any input.

Cheers, m