Indeed, Bristol Uni actually does a separate Avionics Systems course (shameless plug...) with this in mind, which is then shared across computer science, electrical engineering and aeronautical engineering. The aeronautical eng. then still covers your basic electronics and programming though.
However a word of warning on such things, firstly such courses do not include things like aerodynamics, structures and materials, so candidates should be prepared to be essentially working as a specialist programmer / electrical engineer.
Secondly there are quite a few companies out there that do not look for avionics engineers but instead look for physicists or more classical Aeronautical / Aerospace engineers. Why? Well who in HR has ever heard of avionics... The exception seems to be BAES who have a thing for avionics.