`promoters()` fails on `GPos` objects
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1
Entering edit mode
@charles-plessy-7857
Last seen 19 hours ago
Japan

Hello,

promoters() fails on GPos objects; is that expected? If yes, maybe the error message could be made more friendly, for instance by suggesting to use promoters(GRanges(x)).

> gpos1a <- GPos(seqnames=Rle(c("chr1", "chr2", "chr1"), c(10, 6, 4)),
+                pos=c(44:53, 5:10, 2:5))
> gpos1a
UnstitchedGPos object with 20 positions and 0 metadata columns:
       seqnames       pos strand
          <Rle> <integer>  <Rle>
   [1]     chr1        44      *
   [2]     chr1        45      *
   [3]     chr1        46      *
   [4]     chr1        47      *
   [5]     chr1        48      *
   ...      ...       ...    ...
  [16]     chr2        10      *
  [17]     chr1         2      *
  [18]     chr1         3      *
  [19]     chr1         4      *
  [20]     chr1         5      *
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
> promoters(gpos1a)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘update_ranges’ for signature ‘"UnstitchedIPos"’
> sessionInfo()
R Under development (unstable) (2021-10-27 r81107)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bookworm/sid

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GenomicRanges_1.47.4 GenomeInfoDb_1.31.1  IRanges_2.29.0       S4Vectors_0.33.2     BiocGenerics_0.41.1 

loaded via a namespace (and not attached):
[1] zlibbioc_1.41.0        compiler_4.2.0         XVector_0.35.0         tools_4.2.0            GenomeInfoDbData_1.2.7 RCurl_1.98-1.5         bitops_1.0-7

Have a nice day,

Charles

GenomicRanges • 118 views
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3
Entering edit mode
@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States

Hi Charles,

This is now addressed in GenomicRanges 1.47.5 (devel) and 1.46.1 (release). Both versions should propagate to the public repos and become available via BiocManager::install() in the next 24 hours in devel and next 72 hours in release.

Generally speaking, GPos objects still lack a few GRanges functionalities but the gap is slowly closing.

Cheers,

H.

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