Error printing a CompressedGRangesList
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@lluis-revilla-sancho
Last seen 15 days ago
European Union

I'm trying to annotate some data from a Bisulphite experiment, from which I have a GRanges object without any annotation:

GRanges object with 872900 ranges and 0 metadata columns:
           seqnames    ranges strand
              <Rle> <IRanges>  <Rle>
       [1]    chr10     48196      *
       [2]    chr10     48486      *
       [3]    chr10     49247      *
       [4]    chr10     49258      *
       [5]    chr10     49595      *
       ...      ...       ...    ...
  [872896]     chrY  26439351      *
  [872897]     chrY  56866730      *
  [872898]     chrY  56871726      *
  [872899]     chrY  56879863      *
  [872900]     chrY  56885734      *
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths

I'm pulling annotation data from TxDb.Hsapiens.UCSC.hg19.knownGene to annotate each position with promoters and genes.
Before using nearest, findOverlaps, ... I thought to collect the information in a single object with sensible names for the other researchers.
But when I combine the resulting object there is an error that prevents me checking the output:

suppressPackageStartupMessages(library("TxDb.Hsapiens.UCSC.hg19.knownGene"))
genes <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene, column = "gene_id",
               single.strand.genes.only=FALSE)
genes <- sort(genes)
promoters <- promoters(TxDb.Hsapiens.UCSC.hg19.knownGene, column = "gene_id")
promoters <- sort(promoters)
gp <- c(genes, promoters)
gp
#> GRangesList object of length 106419:
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'show': error in evaluating the argument 'x' in selecting a method for function 'as.list': subscript is a NSBS object that is incompatible with the current
#>   subsetting operation

Created on 2023-01-03 with reprex v2.0.2

PS: I would appreciate any suggestion that helped me annotate and existing GRanges with annotation data.
I am probably missing something as I haven't found HOWTOs or vignettes documenting how to do this.

GenomicRanges • 856 views
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Entering edit mode
@lluis-revilla-sancho
Last seen 15 days ago
European Union

The maintainer reported that it is fixed: "Should be fixed in S4Vectors 0.36.2 (release) and 0.37.4 (devel)."

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