Questions Regarding Parameter Settings in FUNKI

[NathalieReilly]

Hello!

I have been using the RShiny app to run FUNKI, it’s a super useful tool and I really like using it! But I have a couple of questions regarding some of the parameters. I was wondering if someone could help me? I am using FUNKI to run DoRothEA to find transcription factor footprints in an RNA seq dataset I have generated.

My main question is on setting the regulon minimal size. By default it’s set to 5 but I read some articles where they set the minimal size to 25. I was wondering if you could give me any guidance on how to determine this number?

Furthermore I always leave the method for computing signatures at “none” which is also the default setting. Could you also explain to me what this does and how it would change my result if I set it to something different?