plyranges select() when a metadata column is shared with core variable
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@mikelove
Last seen 1 day ago
United States

I'm using ensembldb to construct some ranges, and then was using select() to select some metadata columns.

I noticed that the transcripts I was working with have a metadata column width, not the same as the width of the range. This then interferes with select():

> gr <- GRanges("chr1",IRanges(1:3,width=10))
> mcols(gr)$width <- 7
> mcols(gr)$test <- 0
> mcols(gr)$test2 <- "a"
> gr
GRanges object with 3 ranges and 3 metadata columns:
      seqnames    ranges strand |     width      test       test2
         <Rle> <IRanges>  <Rle> | <numeric> <numeric> <character>
  [1]     chr1      1-10      * |         7         0           a
  [2]     chr1      2-11      * |         7         0           a
  [3]     chr1      3-12      * |         7         0           a
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> gr %>% select(test2)
GRanges object with 3 ranges and 1 metadata column:
      seqnames    ranges strand |     test2
         <Rle> <IRanges>  <Rle> | <numeric>
  [1]     chr1      1-10      * |         0
  [2]     chr1      2-11      * |         0
  [3]     chr1      3-12      * |         0
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

This is using current release/devel branch.

I wonder if select() should complain about metadata columns with names shared with core variables at the outset to avoid this issue?

plyranges • 175 views
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Another select() issue, I think the error here could be instead about the missing metadata column:

> gr <- as_granges(data.frame(seqnames=1,start=1,end=100,foo=7))
> gr
GRanges object with 1 range and 1 metadata column:
      seqnames    ranges strand |       foo
         <Rle> <IRanges>  <Rle> | <numeric>
  [1]        1     1-100      * |         7
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> gr %>% select(bar)
Error in select_rng(.data, .drop_ranges, ...) :
  Cannot select/rename the following columns: seqnames, start, end, width, strand
Calls: %>% -> select -> select.Ranges -> select_rng
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