I read the CENTIPEDE manuscript. I think the author scanned all putative TFBS across the genome. However, in your tutorial, you suggested using FIMO only to obtain TFBS in peak regions.

fimo_res <- read.table("./fimo_Foxp3_in_Treg_ATAC/fimo.txt", stringsAsFactors = F) #fimo.txtへのパスを指定 ...