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Visible light communication (VLC) is envisioned as a core component of future wireless communication networks due to, among others, the huge unlicensed bandwidth it offers and the fact that it does not cause any interference to existing radio frequency (RF) communication systems. Most research on RF and VLC coexistence has focused on hybrid designs where data transmission to any user could originate from either an RF or a VLC access point (AP). However, hybrid RF/VLC systems fail to exploit the distinct transmission characteristics of RF and VLC systems to fully reap the benefits they can offer. Aggregated RF/VLC systems, in which any user can be served simultaneously by both RF and VLC APs, have recently emerged as a more promising and robust design for the coexistence of RF and VLC systems. To this end, this paper, for the first time, investigates AP assignment, subchannel allocation (SA), and transmit power allocation (PA) to optimize the energy efficiency (EE) of aggregated RF/VLC systems while considering the effects of interference and VLC line-of-sight link blockages. A novel and challenging EE optimization problem is formulated for which an efficient joint solution based on alternating optimization is developed. More particularly, an energy-efficient AP assignment algorithm based on matching theory is proposed. Then, a low-complexity SA scheme that allocates subchannels to users based on their channel conditions is developed. Finally, an effective PA algorithm is presented by utilizing the quadratic transform approach and a multi-objective optimization framework. Extensive simulation results reveal that: 1) the proposed joint AP assignment, SA, and PA solution obtains significant EE, sum-rate, and outage performance gains with low complexity, and 2) the aggregated RF/VLC system provides considerable performance improvement compared to hybrid RF/VLC systems.