GSEA in R

[Vishakha Kurlawala]

Hello, 

I am trying to perform GSEA in R using the GSEA function from the Cluster Profiler library. I am new to R and it is necessary that I perform the GSEA on R. I am having issues understanding the TERM2GENE argument. If anyone here could help me out, that would be greatly appreciated. 

I am performing GSEA for a proteomics dataset and my genelist has been generated and sorted. The genelist has the log2FC and protein Ids. 

Thank you!

[Anthony Castanza]

Hello,

 

ClusterProfiler contains a third party reimplementation of GSEA and we unfortunately do not provide support for it, and cannot vouch for its functionality. The ClusterProfiler devleoper's page is here: https://guangchuangyu.github.io/software/clusterProfiler/ and the manual on Bioconductor is here: https://bioconductor.org/packages/release/bioc/manuals/clusterProfiler/man/clusterProfiler.pdf

 

We don't provide an official R version of GSEA, however GSEA is command line scriptable if it isn't 100% necessary that R be used directly. We do have an unofficial R version of GSEA here: https://github.com/GSEA-MSigDB/GSEA_R but it isn't recommended for "production" workloads and would strongly urge the Desktop or Command line implementations available from the https://gsea-msigdb.org downloads page.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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