[BioC] Replacing GRanges mcol makes it inaccessible

[Shraddha Pai]

Hi all,
After I update the metadata on a Granges() object, I can no longer access
the object. This happens on a Granges() object generated from the GFF3
file; I don't know if that matters.

Here is the code to reproduce the error message. The gff file in question
is from miRbase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/hsa.gff3

Has anyone else experienced this problem? Is there something different
about a GRanges object generated by import()?
I have also tried first setting mcols() to NULL and then doing mcols(x) <-
tmp (putting in my new content), but that results in the same error.

Thanks in advance,
Shraddha 
-----
Shraddha Pai, Ph.D.
Post-doctoral fellow
Krembil Family Epigenetic Research Laboratory (Lab head: Dr. Art Petronis)
Centre for Addiction and Mental Health, Toronto

-------------------------------------------


> require(rtracklayer)
> x <- import("hsa.gff3")
> tmp <- mcols(x)
> tmp <- cbind(as.data.frame(tmp), new_column="abc")
> head(x)
GRanges with 6 ranges and 8 metadata columns:
      seqnames           ranges strand |   source                     type
         <Rle>        <IRanges>  <Rle> | <factor>                 <factor>
  [1]     chr1 [ 17369,  17436]      - |     <NA> miRNA_primary_transcript
  [2]     chr1 [ 17409,  17431]      - |     <NA>                    miRNA
  [3]     chr1 [ 17369,  17391]      - |     <NA>                    miRNA
  [4]     chr1 [ 30366,  30503]      + |     <NA> miRNA_primary_transcript
  [5]     chr1 [ 30438,  30458]      + |     <NA>                    miRNA
  [6]     chr1 [567705, 567793]      - |     <NA> miRNA_primary_transcript
          score     phase           ID           Alias            Name
      <numeric> <integer>  <character> <CharacterList>     <character>
  [1]      <NA>      <NA>    MI0022705       MI0022705  hsa-mir-6859-1
  [2]      <NA>      <NA> MIMAT0027618    MIMAT0027618 hsa-miR-6859-5p
  [3]      <NA>      <NA> MIMAT0027619    MIMAT0027619 hsa-miR-6859-3p
  [4]      <NA>      <NA>    MI0006363       MI0006363  hsa-mir-1302-2
  [5]      <NA>      <NA> MIMAT0005890    MIMAT0005890    hsa-miR-1302
  [6]      <NA>      <NA>    MI0022558       MI0022558    hsa-mir-6723
      Derives_from
       <character>
  [1]         <NA>
  [2]    MI0022705
  [3]    MI0022705
  [4]         <NA>
  [5]    MI0006363
  [6]         <NA>
  ---
  seqlengths:
    chr1 chr10 chr11 chr12 chr13 chr14 ...  chr6  chr7  chr8  chr9  chrX
chrY
      NA    NA    NA    NA    NA    NA ...    NA    NA    NA    NA    NA
 NA
> mcols(x) <- tmp
> head(x)
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'extractROWS' for
signature '"AsIs"'
> x
GRanges with 4665 ranges and 9 metadata columns:
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'extractROWS' for
signature '"AsIs"'

----
Here is the output from sessionInfo()
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] rtracklayer_1.22.2   GenomicRanges_1.14.4 XVector_0.2.0
[4] IRanges_1.20.6       BiocGenerics_0.8.0

loaded via a namespace (and not attached):
[1] BSgenome_1.30.0   Biostrings_2.30.1 RCurl_1.95-4.1    Rsamtools_1.14.2
[5] XML_3.98-1.1      bitops_1.0-6      stats4_3.0.1      tools_3.0.1
[9] zlibbioc_1.8.0