Here are few questions/suggestions for our experts on range operations:
(1) Are there currently accessor functions available to extract the range data of the following feature types from TxDb objects: miRNAs, rRNAs, tRNAs and transposons? The existing functions (e.g. microRNA) for some of these features seem to depend on other databases (e.g. miRbase) which are not very useful for more recently sequenced organisms where all we usually have is a fasta sequence file and a gff/gtf annotation file. Since the above features are usually encoded in most gff/gtf files it would be nice if they were retrievable from TxDb objects as well.
(2) A simple accessor function for obtaining intergenic ranges from TxDb objects would also be useful. Right now I only know how to obtain this range type in several steps by (i) extracting transcripts by genes, (ii) flattening the overlapping ones with reduce() and then applying gaps() to obtain the non-annotated regions. Having an explicit function, similar to promoter() or intron(), for this routine would be useful and minimize errors often made by less experienced users.