I want to use ReactomePA package for reactome pathway analysis.
Problem is, It takes EntrezID as input. Is there a way to use ReactomePA with Gene Symbols.
I know that I can map Gene Symbols with EntrezID, but I don't want to do that. I want to run analysis with Gene Symbols.

gene symbol is for human, while entrez gene ID for computer.

You can use bitr function in clusterProfiler to convert gene symbol to entrez gene ID. See the example in vignette,

http://bioconductor.org/packages/3.2/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

Dear Deepak,

i dont understand the reason why you don't want to use EntrezIDs instead of Gene Symbols. Anyway, if you are still willing to use as input Gene Symbols, then you could use the web tool Enrichr, which includes a gene-set library for Reactome 2015:  http://amp.pharm.mssm.edu/Enrichr/ . It uses also various scoring methods to compute enrichment.

Best,

Efstathios

Hi,

You can just add this line

 GeneID<- unname(unlist(translate(GeneList, org.Hs.egSYMBOL2EG)))

Karim