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extracting gene names from clusterProfiler following gseGO

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?

clusterprofiler
• 2,127 views • link
updated by Basti • Basti • written by Elizabeth Alice • Elizabeth Alice

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.

• 0 views • link
written by rpolicastro rpolicastro

1 answer

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

• 0 views • link
written by Basti • Basti

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