[Bioc-devel] Txdb Issues - all exon names are NA's ?

[Hervé Pagès]

Hi Sonali,

UCSC doesn't provide names for the exons of their gene models.
See the table where this data is coming from:

 
https://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=genes&hgta_track=knownGene&hgta_table=knownGene&hgta_doSchema=describe+table+schema

The exon information is all coming from the exonStarts and exonEnds
columns. No exon names!

H.

PS: Maybe this would better be asked on the support site.

On 09/22/2015 04:44 PM, Arora, Sonali wrote:
>   Hi everyone,
>
> I was trying to get the exons by gene from a txdb object but I get NA's
> for all exon_name's. Please advise.
>
>  > library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>  > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>  > ebg2 <- exonsBy(txdb, by="gene")
>  >
>  > ebg2
> GRangesList object of length 23459:
> $1
> GRanges object with 15 ranges and 2 metadata columns:
>         seqnames               ranges strand   |   exon_id
>            <Rle>            <IRanges>  <Rle>   | <integer>
>     [1]    chr19 [58858172, 58858395]      -   |    250809
>     [2]    chr19 [58858719, 58859006]      -   |    250810
>     [3]    chr19 [58859832, 58860494]      -   |    250811
>     [4]    chr19 [58860934, 58862017]      -   |    250812
>     [5]    chr19 [58861736, 58862017]      -   |    250813
>     ...      ...                  ...    ... ...       ...
>    [11]    chr19 [58868951, 58869015]      -   |    250821
>    [12]    chr19 [58869318, 58869652]      -   |    250822
>    [13]    chr19 [58869855, 58869951]      -   |    250823
>    [14]    chr19 [58870563, 58870689]      -   |    250824
>    [15]    chr19 [58874043, 58874214]      -   |    250825
>           exon_name
>         <character>
>     [1]        <NA>
>     [2]        <NA>
>     [3]        <NA>
>     [4]        <NA>
>     [5]        <NA>
>     ...         ...
>    [11]        <NA>
>    [12]        <NA>
>    [13]        <NA>
>    [14]        <NA>
>    [15]        <NA>
>
> $10
> GRanges object with 2 ranges and 2 metadata columns:
>        seqnames               ranges strand | exon_id exon_name
>    [1]     chr8 [18248755, 18248855]      + |  113603      <NA>
>    [2]     chr8 [18257508, 18258723]      + |  113604      <NA>
>
> ...
> <23457 more elements>
> -------
> seqinfo: 93 sequences (1 circular) from hg19 genome
>  > testgr <- unlist(ebg2)
>  > table(is.na(mcols(testgr)$exon_name))
>
>    TRUE
> 272776
>  > sessionInfo()
> R version 3.2.2 RC (2015-08-09 r68965)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices utils
> [7] datasets  methods   base
>
> other attached packages:
> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.1
> [2] GenomicFeatures_1.21.29
> [3] AnnotationDbi_1.31.18
> [4] Biobase_2.29.1
> [5] GenomicRanges_1.21.28
> [6] GenomeInfoDb_1.5.16
> [7] IRanges_2.3.21
> [8] S4Vectors_0.7.18
> [9] BiocGenerics_0.15.6
>
> loaded via a namespace (and not attached):
>   [1] XVector_0.9.4              zlibbioc_1.15.0
>   [3] GenomicAlignments_1.5.17   BiocParallel_1.3.52
>   [5] tools_3.2.2                SummarizedExperiment_0.3.9
>   [7] DBI_0.3.1                  lambda.r_1.1.7
>   [9] futile.logger_1.4.1        rtracklayer_1.29.27
> [11] futile.options_1.0.0       bitops_1.0-6
> [13] RCurl_1.95-4.7             biomaRt_2.25.3
> [15] RSQLite_1.0.0              Biostrings_2.37.8
> [17] Rsamtools_1.21.17          XML_3.98-1.3
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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