I am trying to work with some very large BED Files obtained from GEO of ChIP-Seq results (Specifically - this data here). There are a few BED Files that I am hoping to visualize in addition to the MAC Peaks that were called. I wanted to try to use BioConductor to do this, but the BED Files (which contain upwards of 24 million aligned reads) cause R to choke. I am just starting with BioConductor.
What's the best way to visualize the reads with the peaks (called by MACS)? Is this something that can be done with BioConductor?