Question: pre-ranked GSEA within R: options?
gravatar for Daniel Schmolze
4.9 years ago by
Daniel Schmolze20 wrote:
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.
ADD COMMENTlink modified 4 months ago by atakanekiz20 • written 4.9 years ago by Daniel Schmolze20
gravatar for predeus
21 months ago by
United States
predeus0 wrote:

use fgsea package on Bioconductor

ADD COMMENTlink written 21 months ago by predeus0
gravatar for atakanekiz
4 months ago by
atakanekiz20 wrote:

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.

ADD COMMENTlink written 4 months ago by atakanekiz20
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