How to extract all the terms using summary?
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.
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Guangchuang Yu
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xieshaojun0621
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xieshaojun0621
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If you set pvalueCutoff=1 and qvalueCutoff=1, of course all result will return. Not matter it is significant or not.
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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.