[BioC] BUG in Genomic(Features|Ranges): names(unlist(transcriptsBy(txdb, 'gene'))) is UNRELIABLE!!!

[Martin Morgan]

On 08/31/2012 10:07 PM, Cook, Malcolm wrote:
> Careful fellow travelers,
>
> I find that unlisting the GenomicRanges returned from a call to `transcriptsBy` returns a list with names that are gene names... only they are incorrect!
>
> Look:
>
>> txdb<-makeTranscriptDbFromBiomart(biomart="ensembl", dataset="dmelanogaster_gene_ensembl")
> ...
>> transcriptsBy(txdb,'gene')[2]
> GRangesList of length 1:
> $FBgn0000008
> GRanges with 3 ranges and 2 elementMetadata cols:
>        seqnames               ranges strand |     tx_id     tx_name
>           <Rle>            <IRanges>  <Rle> | <integer> <character>
>    [1]       2R [18024494, 18060339]      + |      8616 FBtr0100521
>    [2]       2R [18024496, 18060346]      + |      8615 FBtr0071763
>    [3]       2R [18024938, 18060346]      + |      8617 FBtr0071764
> ...
>> unlist(transcriptsBy(txdb,'gene')[2])
> GRanges with 3 ranges and 2 elementMetadata cols:
>                 seqnames               ranges strand |     tx_id     tx_name
>                    <Rle>            <IRanges>  <Rle> | <integer> <character>
>     FBgn0000008       2R [18024494, 18060339]      + |      8616 FBtr0100521
>    FBgn00000081       2R [18024496, 18060346]      + |      8615 FBtr0071763
>    FBgn00000082       2R [18024938, 18060346]      + |      8617 FBtr0071764
> ...
>
>
> Arguably, those names on the the GRanges should either all be the same, namely FBgn0000008, or they should not be returned.

This is the way unlist works in base R

 > unlist(list(a=1:2))
a1 a2
  1  2

but the behavior has been changed in devel (to be release in early October)

 > unlist(GRangesList(A=GRanges("a", IRanges(1:2, 10))))
GRanges with 2 ranges and 0 metadata columns:
     seqnames    ranges strand
        <Rle> <IRanges>  <Rle>
   A        a   [1, 10]      *
   A        a   [2, 10]      *
   ---
   seqlengths:
     a
    NA

the work-around, as in base R, is to add use.names=FALSE to unlist 
(perhaps adding a metadata column of rep(names(txdb), 
elementLengths(txdb))).

> This 'bug' has been around for a some time.  I meant to report it, and just tripped over it again.
>
> Can fix?
>
> Thanks!
>
> Malcolm
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (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] tools     splines   parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] igraph_0.6-2          log4r_0.1-4           vwr_0.1               RecordLinkage_0.4-1   ffbase_0.5            ff_2.2-7              bit_1.1-8             evd_2.2-7             ipred_0.8-13          prodlim_1.3.1         KernSmooth_2.23-8     nnet_7.3-4            survival_2.36-14      mlbench_2.1-1         MASS_7.3-20           ada_2.0-3             rpart_3.1-54          e1071_1.6             class_7.3-4           XLConnect_0.2-0       XLConnectJars_0.2-0   rJava_0.9-3           latticeExtra_0.6-19   RColorBrewer_1.0-5    lattice_0.20-6        doMC_1.2.5            multicore_0.1-7
> [28] SRAdb_1.10.0          RCurl_1.91-1          bitops_1.0-4.1        graph_1.34.0          BSgenome_1.24.0       rtracklayer_1.16.3    Rsamtools_1.8.6       Biostrings_2.24.1     GenomicFeatures_1.8.2 AnnotationDbi_1.19.31 GenomicRanges_1.8.12  R.utils_1.16.0        R.oo_1.9.8            R.methodsS3_1.4.2     IRanges_1.14.4        Biobase_2.17.7        BiocGenerics_0.3.1    data.table_1.8.2      compare_0.2-3         svUnit_0.7-10         doParallel_1.0.1      iterators_1.0.6       foreach_1.4.0         ggplot2_0.9.1         sqldf_0.4-6.4         RSQLite.extfuns_0.0.1 RSQLite_0.11.1
> [55] chron_2.3-42          gsubfn_0.6-4          proto_0.3-9.2         DBI_0.2-5             functional_0.1        reshape_0.8.4         plyr_1.7.1            stringr_0.6.1         gtools_2.7.0
>
> loaded via a namespace (and not attached):
>   [1] biomaRt_2.12.0   codetools_0.2-8  colorspace_1.1-1 compiler_2.15.0  dichromat_1.2-4  digest_0.5.2     GEOquery_2.23.5  grid_2.15.0      labeling_0.1     memoise_0.1      munsell_0.3      reshape2_1.2.1   scales_0.2.1     stats4_2.15.0    tcltk_2.15.0     XML_3.9-4        zlibbioc_1.2.0
>>


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