Hello,

I want to enrich KEGG pathways on my rice genes. I tried "clusterProfiler", but its input is entrezID and my gene ids are RAPIDs (Os02g0617800). I want to keep using the RAPIDs, so I have to write my own enrichment functions. To do this, I need the mapping between RAPIDs and pathways. How to get the mapping from KEGGRSET?

Regards.

You don't need to convert your IDs. KEGG already provides a mapping between the Japanese rice genome pathways and RAPIDs.

For example, you can use the kegga function in the limma package with species.KEGG="dosa" and it will use RAPIDs directly. To see which RAPIDs KEGG is using, have a look at the gene to pathway annotation:

> library(limma)
> GK <- getGeneKEGGLinks(species.KEGG="dosa")
> head(GK)
           GeneID      PathwayID
1 Os01t0118000-01 path:dosa00010
2 Os01t0147900-01 path:dosa00010
3 Os01t0160100-01 path:dosa00010
4 Os01t0190400-01 path:dosa00010
5 Os01t0191700-01 path:dosa00010
6 Os01t0276700-01 path:dosa00010

Alternatively, to get NCBI Entrez Gene IDs instead:

> GK.Entrez <- getGeneKEGGLinks(species.KEGG="osa")
> head(GK.Entrez)
     GeneID     PathwayID
1 107275630 path:osa00010
2 107277365 path:osa00010
3   4324066 path:osa00010
4   4324263 path:osa00010
5   4324666 path:osa00010
6   4325027 path:osa00010