Question: Performing GSEA using MSigDB gene sets in R
3
gravatar for wilsonav
22 months ago by
wilsonav30
wilsonav30 wrote:

I am trying to perform a gene set enrichment analysis in r using the gene sets available from msigdb and a list of gene names from my own data set.

I am able to to use the msigdbr library to import the gene collections from msigdb into r, but I am unsure of how to specifically use a function to compute the overlaps between the genes in my gene set and the gene sets in msigdb and obtain the FDR p-values. Are there any tutorials online for this method or example codes?

Thank you

gsea R msigdb • 4.2k views
ADD COMMENTlink modified 22 months ago by igor11k • written 22 months ago by wilsonav30
4
gravatar for igor
22 months ago by
igor11k
United States
igor11k wrote:

You can try the fgsea package, which is probably most similar to the original GSEA. It can be run in a single command:

fgseaRes <- fgsea(pathways = examplePathways,  stats = exampleRanks)

Check the vignette for more details: https://www.bioconductor.org/packages/devel/bioc/vignettes/fgsea/inst/doc/fgsea-tutorial.html

There is also an example in the msigdbr vignette: https://cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html

ADD COMMENTlink modified 5 months ago • written 22 months ago by igor11k
1

It's worth noting that fgsea is similar to GSEA-Preranked rather than to the original GSEA method published in the GSEA articles that used sample permutation.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Gordon Smyth1.8k

Yes. Until very recently, the recommendation from GSEA developers was to use the pre-ranked GSEA for RNA-seq data, so that has been the default one in my mind since most transcriptomic data is RNA-seq.

ADD REPLYlink written 6 weeks ago by igor11k

OK. It's an important issue because GSEA-preranked doesn't give proper FDR control (and hasn't been claimed to do so by the GSEA developers as far as I know).

ADD REPLYlink written 6 weeks ago by Gordon Smyth1.8k
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