Question: Performing GSEA using MSigDB gene sets in R
1
gravatar for wilsonav
6 months ago by
wilsonav10
wilsonav10 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 • 733 views
ADD COMMENTlink modified 6 months ago by igor7.6k • written 6 months ago by wilsonav10
3
gravatar for igor
6 months ago by
igor7.6k
United States
igor7.6k 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

ADD COMMENTlink written 6 months ago by igor7.6k
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