Ignoring negative positions when intersecting two GRanges objects

[csoneson]

Hi,

I ran into a behaviour that was unexpected to me, and wanted to check if it is intended (I didn't see any mention of it in the documentation, apologies if I missed it somewhere). We're sometimes working with ranges with negative coordinates (e.g., relative to a specific landmark), and the following works as expected:

> a <- IRanges(start = -5, end = 5)
> b <- IRanges(start = -10, end = 10)
> intersect(a, b)
IRanges object with 1 range and 0 metadata columns:
          start       end     width
      <integer> <integer> <integer>
  [1]        -5         5        11

However, for GRanges objects, intersect discards all negative coordinates:

> a <- GRanges(seqnames = "chr1", IRanges(start = -5, end = 5))
> b <- GRanges(seqnames = "chr1", IRanges(start = -10, end = 10))
> intersect(a, b)
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1       1-5      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

Specifying seqlengths doesn't seem to make any difference, nor designating the chromosome as circular.

pintersect, on the other hand, keeps the negative coordinates for GRanges objects:

> pintersect(a, b)
GRanges object with 1 range and 1 metadata column:
      seqnames    ranges strand |       hit
         <Rle> <IRanges>  <Rle> | <logical>
  [1]     chr1      -5-5      * |      TRUE
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

However, here I noticed another thing that was slightly counterintuitive. While the following looks like I would expect:

> a <- GRanges(seqnames = "chr1", IRanges(start = c(-3, 5, 12), end = c(6, 12, 15)))
> b <- GRanges(seqnames = "chr1", IRanges(start = -10, end = 10))
> pintersect(a, b, drop.nohit.ranges = TRUE)
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1      -3-6      *
  [2]     chr1      5-10      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

if I change the last range in a to start at position 11 (still not overlapping b) it would not be dropped:

> a <- GRanges(seqnames = "chr1", IRanges(start = c(-3, 5, 11), end = c(6, 12, 15)))
> b <- GRanges(seqnames = "chr1", IRanges(start = -10, end = 10))
> pintersect(a, b, drop.nohit.ranges = TRUE)
GRanges object with 3 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1      -3-6      *
  [2]     chr1      5-10      *
  [3]     chr1     11-10      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

Session info

R Under development (unstable) (2025-01-03 r87521)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.2

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Zurich
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicRanges_1.59.1 GenomeInfoDb_1.43.2  IRanges_2.41.2       S4Vectors_0.45.2     BiocGenerics_0.53.3 
[6] generics_0.1.3      

loaded via a namespace (and not attached):
[1] httr_1.4.7              compiler_4.5.0          R6_2.5.1                XVector_0.47.2         
[5] tools_4.5.0             GenomeInfoDbData_1.2.13 rstudioapi_0.17.1       UCSC.utils_1.3.1       
[9] jsonlite_1.8.9