How to extract all the terms using summary?

Question

[xieshaojun0621]

Hi there! I'm using clusterProfiler to do KEGG enrichment analysis. The function "enricher" was used.

res <- enricher(geneList, TERM2GENE=term2gene, TERM2NAME=term2name, pvalueCutoff = 1, pAdjustMethod = "BH", qvalueCutoff = 1)

Then the function "summary" was used to extract the results.

summary(res)

But only significant ones were returned. I'm wondering whether there is a way to output all the terms rather than just significant ones. Thanks.

clusterProfiler_3.0.5 and DOSE_2.10.7 were used.

[EagleEye]

Have you tried GeneSCF ? Which returns all the significant and non-significant terms. Additionally you can also download complete KEGG terms with corresponding genes as simple text file using GeneSCF.

Answer 1

[Guangchuang Yu]

If you set pvalueCutoff=1 and qvalueCutoff=1, of course all result will return. Not matter it is significant or not.