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Question: how to perform pre ranked GSEA in R?
1
gravatar for Nemo
3.5 years ago by
Nemo80
India
Nemo80 wrote:

I have a list of probes (up regulated genes) and I have a gene set (consists of several column of probes which have been already ranked based on their expression) 

Now, I want to perform  Kolmogorov-smirnov test or pre ranked GSEA. can any body help with how to do it ? you can find an example data in the following links

 

ADD COMMENTlink modified 18 months ago by predeus0 • written 3.5 years ago by Nemo80
0
gravatar for samuel collombet
3.5 years ago by
France
samuel collombet120 wrote:

Hi Nemo,

You can use the topGO package, the vignette shows example on how to do it :)

ADD COMMENTlink written 3.5 years ago by samuel collombet120
0
gravatar for predeus
18 months ago by
predeus0
United States
predeus0 wrote:

use fgsea bioconductor package.

ADD COMMENTlink written 18 months ago by predeus0
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