There are anywhere from 3 to infinity versions of GFF. When rtracklayer
cannot detect the version (from either the filename extension or
#gff-version directive), it assumes GFF version 1. To tell it otherwise,
use the "version" argument. In this case, you want version="2".
But what you have is actually a special subformat of GFF2, called GTF.
rtracklayer could have detected this by the "gtf" extension, or you could
pass format="gtf". It doesn't do anything special with GTF, though.

Maybe what you really want is GenomicFeatures::makeTranscriptDbFromGFF,
which uses rtracklayer to make a TranscriptDb from GFF data. That's
generally more appropriate for representing transcript structures compared
to GRanges.

Michael

On Thu, Oct 31, 2013 at 10:51 PM, chris warth [guest] <
guest@bioconductor.org> wrote:

>
> After reading in a GTF file with rtrackler::import(), I have a GRanges
> object.  How can I select the ranges whose gene_id (or transcript_id) match
> a particular value?
>
> > library(rtracklayer)
> > gtf <- import(system.file("tests", "gtf.gff", package="rtracklayer"),
> asRangedData=F)
>
> I can see the metadata with 'mcols(gtf)', and I can even see the gene_id
> with 'mcols(gtf)$group',
>
> > mcols(gtf)$group
> [1] gene_id "ENSMUSG00000033501.1"; transcript_id "ENSMUST00000040592.1";
> exon_id "ENSMUSE00000310143.1";
> [omitted]
> 3 Levels: gene_id "ENSMUSG00000033501.1"; transcript_id
> "ENSMUST00000040592.1"; exon_id "ENSMUSE00000310143.1"; ...
>
> but I don't see any way to utilize the name=value strings in the group
> column.
>
> Do I just have to parse the values group column myself?
>
> Thanks in advance for any help.
>
>
>  -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] rtracklayer_1.20.4   GenomicRanges_1.12.5 IRanges_1.18.4
> BiocGenerics_0.6.0   BiocInstaller_1.10.4
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.28.0 bitops_1.0-6      BSgenome_1.28.0   RCurl_1.95-4.1
>  Rsamtools_1.12.4  stats4_3.0.2
> [7] tools_3.0.2       XML_3.95-0.2      zlibbioc_1.6.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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