Question

pre-ranked GSEA within R: options?

1

Entering edit mode

Daniel Schmolze ▴ 20

@daniel-schmolze-6341

Last seen 10.2 years ago

I want to do a GSEA entirely from within R, using genes ranked by my own metric. At the moment I'm saving my ranked genes to a .rnk file, then calling Broad's GSEA java program, then reading the resulting output back into R (all I care about are the p-values in gsea_report_for_na_pos_####.xls and gsea_report_for_na_neg_####.xls). Cumbersome to say the least. As far as I can tell, the Broad GSEA R script won't accept pre-ranked genes, but maybe I'm wrong? If not, I'm interested in other options. I'd like to specifically stick with the Broad GSEA algorithm if possible.

• 1.9k views

ADD COMMENT • link updated 6.4 years ago by atakanekiz ▴ 30 • written 10.9 years ago by Daniel Schmolze ▴ 20

score 0 · Answer 1 · 2017-03-10

0

Entering edit mode

predeus • 0

@predeus-9207

Last seen 4.6 years ago

United States

use fgsea package on Bioconductor

ADD COMMENT • link 7.7 years ago predeus • 0

score 0 · Answer 2 · 2018-07-19

I've been playing with GSEA analyses in the last couple of days by using my single cell rnaseq data. I automated sample subsetting, gene ranking (S2N method, but can be replaced by other metrics), performing GSEA (using fgsea package) and reporting the top hits. If you are still interested in this type of analyses, I'm happy to share my code. Let me know.