cluster profiler
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michaelR • 0
@michaelr-9140
Last seen 2 days ago
Switzerland

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)


Thanks a lot for any input.

Cheers, m

clusterProfiler • 72 views
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I noticed that the last line in your code is head(KEGG_enrichment). This (the use of head()) by default will show only the first 6 rows....

What is the output from dim(data.frame(KEGG_enrichment)) and data.frame(KEGG_enrichment) ?