Hej, it is unclear to me how to correctly use the GenomicRanges package for circular genomes, and I failed to find an explanation in vignettes. Assume the following example, in which some intervals are due to eg. shift equal but have a different interval.

library(tidyverse)
library(GenomicRanges)
foo <- GRanges('foo', IRanges(c(-1, 1, 4, 9, 11), width = 5), strand='+')
seqinfo(foo) <- Seqinfo(seqnames = 'foo', isCircular = TRUE, seqlengths = 10)
foo$follow <- follow(foo)
foo$precede <- precede(foo)
findOverlaps(foo, foo, type = 'equal') %>%
  subset(queryHits != subjectHits)
foo

Here, the pairs have different follow/precede rsults, although findOverlaps identified them as identical.

> foo
GRanges object with 5 ranges and 2 metadata columns:
      seqnames    ranges strand |    follow   precede
         <Rle> <IRanges>  <Rle> | <integer> <integer>
  [1]      foo      -1-3      + |      <NA>         3
  [2]      foo       1-5      + |      <NA>         4
  [3]      foo       4-8      + |         1         4
  [4]      foo      9-13      + |         3      <NA>
  [5]      foo     11-15      + |         3      <NA>

Here, the pairs are (1, 4) and (2, 5). These interval are equal yet they have non-zero distances

> distanceToNearest(foo, foo, select='all') %>%
+   as.tibble %>%
+   spread(subjectHits, distance)
# A tibble: 5 x 6
  queryHits   `1`   `2`   `3`   `4`   `5`
      <int> <int> <int> <int> <int> <int>
1         1     0     0     0     5     7
2         2     0     0     0     3     5
3         3     0     0     0     0     2
4         4     5     3     0     0     0
5         5     7     5     2     0     0

What would be the correct approach for nearest neighbor/distances in bioconductor? Thank you in advance.

Hi Adrian,

Thanks for the clear example. It looks like precede(), follow() and the nearest() family don't support circular chromosomes. This is was probably my oversight when these were implemented and it will be fixed soon.

I'm editing my answer because the helpers I suggested won't work on all situations. We are working on a solution and I'll post back when it's implemented.

Valerie