pre-ranked GSEA within R: options?
2
1
Entering edit mode
@daniel-schmolze-6341
Last seen 8.0 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.
• 1.3k views
ADD COMMENT
0
Entering edit mode
predeus • 0
@predeus-9207
Last seen 2.3 years ago
United States

use fgsea package on Bioconductor

ADD COMMENT
0
Entering edit mode
atakanekiz ▴ 30
@atakanekiz-15874
Last seen 4 months ago
Turkey

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 COMMENT

Login before adding your answer.

Traffic: 348 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6