I am wondering what is the intended result of applying promoters to a GRangesList. It seems to be applied to every element within a list element, but I was hoping that it would automatically notice exon_rank and produce one promoter per list element.

> transcripts[1]
GRangesList object of length 1:
$ENST00000496973.5
GRanges object with 6 ranges and 3 metadata columns:
      seqnames              ranges strand |   exon_id         exon_name exon_rank
         <Rle>           <IRanges>  <Rle> | <integer>       <character> <integer>
  [1]     chr1 169795043-169795213      + |     26019 ENSE00001879003.1         1
  [2]     chr1 169798919-169798958      + |     26025 ENSE00003514372.1         2
  [3]     chr1 169800883-169800971      + |     26028 ENSE00003792362.1         3
  [4]     chr1 169802621-169802725      + |     26029 ENSE00003492238.1         4
  [5]     chr1 169803169-169803309      + |     26032 ENSE00003495412.1         5
  [6]     chr1 169804112-169804347      + |     26038 ENSE00001838164.1         6
  -------
  seqinfo: 25 sequences (1 circular) from an unspecified genome; no seqlengths

Promoters doesn't seem to realise that this is a transcript and makes a region surrounding each exon's starting position:

> promoters(transcripts[1])
GRangesList object of length 1:
$ENST00000496973.5
GRanges object with 6 ranges and 3 metadata columns:
      seqnames              ranges strand |   exon_id         exon_name exon_rank
         <Rle>           <IRanges>  <Rle> | <integer>       <character> <integer>
  [1]     chr1 169793043-169795242      + |     26019 ENSE00001879003.1         1
  [2]     chr1 169796919-169799118      + |     26025 ENSE00003514372.1         2
  [3]     chr1 169798883-169801082      + |     26028 ENSE00003792362.1         3
  [4]     chr1 169800621-169802820      + |     26029 ENSE00003492238.1         4
  [5]     chr1 169801169-169803368      + |     26032 ENSE00003495412.1         5
  [6]     chr1 169802112-169804311      + |     26038 ENSE00001838164.1         6
  -------
  seqinfo: 25 sequences (1 circular) from an unspecified genome; no seqlengths

intra-range-methods instructions contain "... GenomicRanges class or one of its subclasses, this includes for example GRanges objects, or a GRangesList object." but further down I see

Arguments x A GenomicRanges object.

(It should probably write GRanges - GenomicRanges is the package name, not the class name). So, I'm not sure what the expected result of applying promoters to a GRangesList is or if should emit an error that it shouldn't be used for a GRangesList at all.