KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
1
0
Entering edit mode
Jessica • 0
@f2701d4f
Last seen 1 hour ago
Australia

Hi! New to bioinformatics here so please forgive me if this is a stupid question.

I am trying to run GSEA on my differential expression dataset using clusterprofiler and the gseKEGG function. I am working on C. perfringens which is a KEGG organism as far as I know. I've put my code below, but basically when I try run the command I hit an error where when it tries to access the URL https://rest.kegg.jp/conv/ncbi-geneid/cpf it fails. My gene list is in Entrez ID format.

gsea_results <- gseKEGG(
  geneList = geneList,
  organism = "cpf",  # KEGG organism code for Clostridium perfringens
  keyType = "ncbi-geneid",
  pvalueCutoff = 0.05
)

Reading KEGG annotation online: "https://rest.kegg.jp/link/cpf/pathway"...
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/cpf"...
Reading KEGG annotation online: "https://rest.kegg.jp/conv/ncbi-geneid/cpf"...
Error in file(con, "r") : 
  cannot open the connection to 'https://rest.kegg.jp/conv/ncbi-geneid/cpf'
In addition: Warning message:
In file(con, "r") :
  cannot open URL 'https://rest.kegg.jp/conv/ncbi-geneid/cpf': HTTP status was '400 Bad Request'

Not sure where to go from here! Again, pretty new to bioinformatics so please keep answers simple and let me know if any other info is required :)

clusterProfiler KEGG • 22 views
ADD COMMENT
0
Entering edit mode
Jessica • 0
@f2701d4f
Last seen 1 hour ago
Australia

Nevermind. Just had to change to Uniprot IDs and it worked :)

ADD COMMENT

Login before adding your answer.

Traffic: 1003 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6