How to compute gsea overlap of gene set with R

Question

[Picasa]

Hi

I would like to compute the overlap of my genes with gene sets, such as MSigDB C8, similar to how it is done on this page:

https://www.gsea-msigdb.org/gsea/msigdb/human/annotate.jsp

In R, I usually use:

library(clusterProfiler)
enricher(my_gene, TERM2GENE = msigdb_C8)

However, I got different results than what is shown on the website. Is there any other R package that I can use?

Answer 1

[Nat.Nataren]

The clusterProfiler enricher() function has a number of arguments you can adjust, perhaps check that you are setting arguments such as pvalueCutoff the same as the threshold used by MSigDB' online GSEA tool. Then you may see better agreement.

    enricher(
gene,
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
universe = NULL,
minGSSize = 10,
maxGSSize = 500,
qvalueCutoff = 0.2,
gson = NULL,
TERM2GENE,
TERM2NAME = NA
)

Documentation that describes the various arguments for clusterProfiler functions is available here. Another R option is the package fgsea.