How to get gseKEGG() to accept an input gene list?

Question

[DN99]

I've got a csv file with 2 columns - one of Entrez IDs and another of gene's measurement/fold-change. I am running code trying to use gseKEGG(), getting the gene list prepared for that function like this:

d <-fread("file.csv")

geneList <- d[,2]
names(geneList) <- as.character(d[,1])
geneList <- sort(geneList, decreasing = TRUE)

Error in `[.data.frame`(x, i) : undefined columns selected

I'm not sure how to work around this error as I can't see what I'm doing wrong here compared to the guidance given to complete this step for gseKEGG() - given here: https://github.com/YuLab-SMU/DOSE/wiki/how-to-prepare-your-own-geneList

What am I missing to get this working?

A snippet of what's in my csv file looks like this (there's no header):

107986084   0.809859097
100874369   0.913054347
100506380   0.423823357
100288797   0.369738668
100137049   0.798110485
100130742   0.78013134
723788  0.764999211
643136  0.231925398
641649  0.317150593
497258  0.754656732

I've also tried just putting a vector of the first column in, which allows me to use sort(), but this outputs:

 kk2 <- gseKEGG(geneList     = geneList,
                organism     = kegg_organism,
                nPerm        = 10000,
                minGSSize    = 3,
                maxGSSize    = 200,
                pvalueCutoff = 0.05,
                pAdjustMethod = "fdr",
                keyType       = "ncbi-geneid")

preparing geneSet collections...
--> Expected input gene ID: 2990,3033,8802,219,131,160287
Error in check_gene_id(geneList, geneSets) : 
  --> No gene can be mapped....

[Hyper_Odin]

gseKEGG() accepts gene list in this pattern hsa04510, which is clearly different from yours.

[DN99]

Thank you for your reply. Does this refer to the keyType setting where you can set it as
one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'? If I am understanding it right my entrez ids should be ok if I've set this to 'ncbi-geneid'. I've also tried to amend my code and had an error from gseKEGG() asking for entrez IDs - I'll amend my question to include this test and in the meantime try another version with KEGG ids.

[Hyper_Odin]

Sorry, for my last answer. Your gene ID seems fine. This is the code i tried with header , and it seems to be working fine.

kegg_gene_list <- list$FC
names(kegg_gene_list) <- list$ID

kegg_gene_list<-na.omit(kegg_gene_list)

kegg_gene_list = sort(kegg_gene_list, decreasing = TRUE)
kegg_organism = "hsa"

kk2 <- gseKEGG(geneList     = kegg_gene_list,
               organism     = kegg_organism,
               nPerm        = 10000,
               minGSSize    = 3,
               maxGSSize    = 800,
               pvalueCutoff = 0.05,
               pAdjustMethod = "none",
               keyType       = "ncbi-geneid")




ID  FC
107986084   0.809859097
100874369   0.913054347
100506380   0.423823357
100288797   0.369738668
100137049   0.798110485
100130742   0.78013134
723788  0.764999211
643136  0.231925398
641649  0.317150593
497258  0.754656732

[DN99]

This has ran for me too - thank you for your help!

[redafazazi]

Hi, I was wondering if you could help me, I have the same kind of problem. Here is the link to my post : gseKEGG - no gene can be mapped (RNAseq analysis)

Thanks!