This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to Load a Molecular Signature Database into clusterProfiler gseGO?

I am using gseGO this way:

gse <- gseGO(geneList=gene_list, 
         ont ="ALL", 
         minGSSize = 3, 
         maxGSSize = 800, 
         pvalueCutoff = 0.05, 
         verbose = TRUE, 
         OrgDb = org.Hs.eg.db, 
         pAdjustMethod = "fdr")

Let's say I want to analyze against a molecular signature on https://www.gsea-msigdb.org/gsea/msigdb/index.jsp. How can I pass this to gseGO? I have tried downloading one of them, reading the read.gmt file and passing as OrgDb.

clusterprofiler rna-seq gsea
• 1,455 views • link
updated by Nitin Narwade Nitin Narwade • written by Manuel Sokolov Ravasqueira • Manuel Sokolov Ravasqueira

I think gseGO uses a pre-built database for the enrichment analysis.

You can use the fgsea package for the geneset enrichment analysis against custom OR mSigDb genesets.

• 0 views • link
written by Nitin Narwade Nitin Narwade

0 answers

No answers yet.

Log in to answer this question.

More posts like this