What is proper enrichKEGG input ids

Question

[MKM]

Question is about function enrichKEGG. Input data is a vector of entrez gene ids. Please see, page 12 of manual at

https://bioconductor.org/packages/release/bioc/manuals/clusterProfiler/man/clusterProfiler.pdf. But for parameter keyType=entrezid is not supported. Its default value is kegg.

That means when one input data it should be in entrezgene ids but downloaded data from Kegg website will consist of kegg ids (not entrez gene ids), can it has any problem during enrichment analysis?

What is the proper command

1)

enrichKEGG( enzids , organism="mmu", keyType = "ENTREZID", use_internal_data = FALSE,
                       pAdjustMethod = "BH", pvalueCutoff  = 0.05, qvalueCutoff  = 0.1)

OR

2)

 enrichKEGG( enzids , organism="mmu", keyType = "kegg", use_internal_data = FALSE,
                       pAdjustMethod = "BH", pvalueCutoff  = 0.05, qvalueCutoff  = 0.1)

Answer 1

[Guangchuang Yu]

first of all, the tag should not contain @.

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according to page 12 that you mentioned, it's very clear of the parameter keyType:

one of "kegg", ’ncbi-geneid’, ’ncib-proteinid’ and ’uniprot’

So, keyType = "ENTREZID" in command 1 is wrong and command 2 will works properly.

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from the post: https://guangchuangyu.github.io/2016/05/convert-biological-id-with-kegg-api-using-clusterprofiler/.

The ‘kegg’ is the primary ID used in KEGG database. The data source of KEGG was from NCBI. A rule of thumb for the ‘kegg’ ID is entrezgene ID for eukaryote species and Locus ID for prokaryotes.

The kegg ID can be entrezgene (as in your example) or Locus or other types. Different species may use different type. We don't make assumption of it and keyType = "ENTREZID" is not accepted.