extracting gene names from clusterProfiler following gseGO

Question

[Elizabeth Alice]

Hello All,

I have run the gseGO function from clusterProfiler.

gse <- gseGO(geneList=gene_list, 
         ont ="MF", 
         keyType = "ENSEMBL", 
         minGSSize = 10, 
         maxGSSize = 800, 
         pvalueCutoff = 0.01, 
         verbose = TRUE, 
         OrgDb = organism, 
         pAdjustMethod = "BH",
         eps = 0)

I have dotplots of the significantly enriched pathways. I would like to extract the gene lists from a certain pathway. I have tried using

 slotNames(gse)
target_genes <- gse@result$geneID[15]

but the resulting object is NULL

15 is the number corresponding to the readout from

gse$Description

I have tried to use other numbers but all are NULL

Does anyone have any ideas?

[rpolicastro]

Going off the top of my head I think you can convert the results to a data.frame using as.data.frame(gse). You then want to filter the row with the correct term, and then one of the columns will have the relevant gene names.

Answer 1

[Basti]

There is no column geneID in gse@result. You need target_genes <- gse@result$core_enrichment[15]