Can anyone share code for doing strand-aware GRanges shifts? I'd like to shift all the ranges in my GrangesList in by one from the regions 5' end.

Thanks!

If you do not mind installing plyranges, its shift_upstream function does it in a simple and readable way.

Example on GRanges:

> GRanges(c("chr1:100-200:+", "chr1:100-200:-")) |> plyranges::shift_upstream(1)
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1    99-199      +
  [2]     chr1   101-201      -
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

You can endoapply it to a GRangesList object like that:

> list(GRanges("chr1:100-200:+"), GRanges("chr1:100-200:-")) |>
+ as("GRangesList") |>
+ endoapply(plyranges::shift_upstream, 1)
GRangesList object of length 2:
[[1]]
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1    99-199      +
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

[[2]]
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1   101-201      -
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

An option using GenomicRanges:

> gr<-GRanges(c("chr1:100-200:+", "chr1:100-200:-"))
> shiftStranded<-function(x, shift=0L,...) GenomicRanges::shift(x ,shift=shift*ifelse('-'==strand(x),-1,1),...)
> shiftStranded(gr ,1)
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1   101-201      +
  [2]     chr1    99-199      -
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> shiftStranded(gr ,c(3,4))
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1   103-203      +
  [2]     chr1    96-196      -
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

edit: add example of how to use shiftStranded on a GRangesList (note use of mendoapply allowing component-specific shifting):

> grl<-GRangesList(list(GRanges(c("chr1:100-200:+","chr1:200-300:-")), GRanges("chr1:100-200:-")))
> mendoapply(shiftStranded,grl ,c(3,4))
GRangesList object of length 2:
[[1]]
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1   103-203      +
  [2]     chr1   197-297      -
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

[[2]]
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1    96-196      -
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths