index setting for different stages of cancer

[XiaoYan000]

Hi, thanks a lot for your amazing tool, it helps me a lot in analysing my cancer genomic project.

While I am struggling to analyze the data with characteristics of different cancer stages (e.g. primary; recurrent), and I have not found if there are some settings that can differentiate them when I run, even if I tried to annotate the stage in "CANCER_TYPE" column, and set the index"-siggroup CANCER_TYPE", it seems no use. Should I seperate the input file by stages?

Looking for your reply!