I'm new to genomic ranges and getting a bit frustrated with it. I'm reading the reference manual and tutorials, but haven't found an answer to the following question:
I've constructed my gr object and assigned sequence lengths to it. I must have made an error, as I'm getting the warning:
In valid.GenomicRanges.seqinfo(x) :
'ranges' contains values outside of sequence bounds. See ?trim to subset ranges.
When I use trim(gr), I simply get back a new gr that is trimmed. But it doesn't show me offending ranges. How can I do that so I can learn where I went wrong in constructing gr in the first place?