GeneActivity based on genebody accessibility

[ZunpengLiu]

Hi,

Thanks for developing and managing this robust tool!

I was wondering if I have a custom gene list and want to calculate the gene activity considering gene body accessibility only. So, I use the addGeneScoreMatrix function with the parameters "extendUpstream = c(0, 0),
extendDownstream = c(0, 0),
geneUpstream = 0,
geneDownstream = 0".

Do you think the parameters can help me achieve my purpose? Do you have any suggestions about this?

Many thanks!

Zunpeng

[rcorces]

Minimally, you also need to set useTSS = FALSE otherwise geneUpstream and geneDownstream dont take effect. With that addition, I think you would accomplish what you are looking for.

[ZunpengLiu]

Thank you so much!

Yes, I also set useTSS = FALSE. I may not fully understand the meaning of extendUpstream and extendDownstream . I wonder if it is reasonable to set them as c(0,0).

[rcorces]

extendUpstream and extendDownstream will have no effect when useTSS = FALSE