Gene set enrichment analysis

Question

[Farha]

I am trying to perform GSEA in R with data from DESeq2(CSV file containing a list of gene names and log2 fold change values)

1- loaded the required packages

2- prepare input (csv file), I extracted the log2 fold change only from the data

3- use gseGO() function from clusterProfiler package to perform GSEA

gse <- gseGO(geneList=gene_list, 
             ont ="ALL", 
             keyType = "ENSEMBL", 
             nPerm = 10000, 
             minGSSize = 3, 
             maxGSSize = 800, 
             pvalueCutoff = 0.05, 
             verbose = TRUE, 
             OrgDb = organism, 
             pAdjustMethod = "none")

4- made Dotplot

require(DOSE)
dotplot(gse, showCategory=10, split=".sign") + facet_grid(.~.sign)

5- and then I am trying to make Encrichment Map

emapplot(gse, showCategory = 10)

but it gives me this error

Error in has_pairsim(x) : 
      Term similarity matrix not available. Please use pairwise_termsim function to deal with the results of enrichment analysis.

[Ram]

The error message is literally telling you what to do.