Hi,

I have a few GRanges that I need to sort based on their chromosomes/seqnames, start and end coordinates of the intervals.

I used to be able to do it in this way:

sort(gr, by = ~ seqnames + start + end)

But now I get this error:

Error in get(nm, parent, mode = "function") :
  object 'seqnames' of mode 'function' was not found

Is there anything wrong with my code?

What's the best way to reliably sort multiple GRanges objects in the same way (similar to bedtools sort or bedops sort-bed)?

Thanks!

Firstly, verify that seqlevels are sorted:

gr <- sortSeqlevels(gr)

Then, just sort your GRanges object:

gr <- sort(gr)

Simple as that. You should take some time follow through the GenomicRanges vignettes. There are a lot of quite useful tricks inside

As long as your seqlevels are ordered correctly, sort() should do it.

> z <- GRanges(c("chr3","chr4","chr1"), IRanges(c(3,4,5), c(6,7,8)))
> seqlevels(z) <- sort(seqlevels(z))
> z
GRanges object with 3 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr3    [3, 6]      *
  [2]     chr4    [4, 7]      *
  [3]     chr1    [5, 8]      *
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths
> sort(z)
GRanges object with 3 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1    [5, 8]      *
  [2]     chr3    [3, 6]      *
  [3]     chr4    [4, 7]      *
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

The error message "object 'seqnames' of mode 'function' was not found" is probably due to the broken sort function. See GRanges manual page 17,

## TODO: Broken. Please fix!

#sort(gr, by = ~ score)

Clearly, sort by mcols was known as broken.