On Fri, May 30, 2014 at 8:48 AM, Shraddha Pai <Shraddha.Pai@camh.ca> wrote:

> 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")
>

I think you want either:
mcols(x)$new_column <-  "abs"
or the shortcut:
x$new_column <-  "abs"

This a bug though; will fix.

> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

