>It's a dataframe attached to ranges. This design extends lower classes like IRanges, and all the accessors, setters, etc are consistent. You can manipulate the range part with integer range operations and manipulate the dataframe part as a dataframe. I would check out the IRanges vignette — this is very helpful.

I agree that the accessors, setters of GRange are consistent. I was having trouble picturing how manipulating the range part impacts the dataframe. I think they are like a database table joint but that is not explicitly spelled out. It becomes even less clear what happens to the attached dataframes when merging two GRange intervals. I once had to a symmetric difference of two GRange and it took a few hours of staring at the manual and trying out things at the command prompt.