Distinction between motifSet and motifPWMs

[sylestiel]

If I were to pull in different motifPWMs databases when running addMotifAnnotations() what should I enter for the motifSet?

For instance if I include homer_pwms, mouse_pwms and encode_pwms what are my options for motifSet= " ? "

Thanks!

[rcorces]

motifSet refers to a pre-defined motif set curated in ArchR. motifPWMs refers to a user-supplied PWMatrixList object.
These two objects are mutually exclusive. You only provide an argument to one of them.
https://www.archrproject.com/reference/addMotifAnnotations.html

[rcorces]

docs updated to make this more clear via 39115e4

[sylestiel]

Thank you!