How to set up the contrast for multiple groups in gseapy.gsea?

[danli349]

Hello:

If the cls file contains more than 2 groups, such as ['parental','parental','s40','s40','s42','s42'], how should I set up the contrast when calling gseapy.gsea if I want to compare parental_vs_s40, parental_vs_s42 and s42_vs_s40?

Thanks a lot

[zqfang]

I think the easiest way to do this is to subset the groups first, then run the gsea . It just two extra line of code you need in python

df_groups = df.loc[,groups]
cls_vector = groups
gsea(...)

[danli349]

I think the easiest way to do this is to subset the groups first, then run the gsea . It just two extra line of code you need in python

df_groups = df.loc[,groups]
cls_vector = groups
gsea(...)

That is great! Thanks