AddMotfiAnnotations for cisbp and JASPAR at the same time

[tzhu-bio]

Is it possible to add cisbp and JASPAR at the same time in AddMotfiAnnotations?

Or can I run peakAnnoEnrichment with cisbp and JASPAR at the same time after I add them in separately.

[rcorces]

As indicated in the function documentation, you can provide a custom set of motifPWMs. So you can do whatever you want.
https://www.archrproject.com/reference/addMotifAnnotations.html

But ArchR does not provide any support for combining two separate motif annotations. You would need to create a combined set of motifPWMs before adding the motif annotations.