It would be useful to have more flexibility in selecting the TSS region. It is currently hardcoded in getGenomicAnnotation that the region is subdivided into 1000 bp regions. For some marks and compact genomes it is too large.
I would like to have a way to specify bins myself, e.g. by specifying a list of breaks like in hist function.
Also: "downstream" category is hardcoded as +3000 bp.
PS. Good package and well-written documentation!