cluster profiler
0
0
Entering edit mode
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)
head(KEGG_enrichment)

Thanks a lot for any input.

Cheers, m

clusterProfiler • 72 views
ADD COMMENT
0
Entering edit mode

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) ?

ADD REPLY

Login before adding your answer.

Traffic: 142 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6