I want to use genomation to annotate previously identified differentially methylated genomic regions and quantify the overall degree of overlap with different gene structures (promoters, TSSs, exons, introns, intergenic).
The annotation file for my specific reference genome is in GFF3 format. Whilst it seems relatively straight forward to use BED 12 format to extract the relevant genomic coordinates using
readTranscriptFeatures() - I can't figure out how to do the same for a GFF3 format annotation file.
I have looked at GenomicFeatures and there it seems possible to extract some of the features listed above (promoters, exons, introns) but this would result in a mix of several GRanges and GRanges list objects and again I have no idea how to combine these objects into the single object of the right format to
plug into annotateWithGeneParts()
Has any one successfully dealt with a similar situation and can give some advice? Alternatively, if anyone can suggest another annotation strategy that would also be gratefully received?