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

[Marc Carlson]

Herve is right. UCSC doesn't give us this information,  And actually, I
think it's pretty rare to see exon names from anybody.   So it's weird to
me that they are a default return value for this method.

  Marc

On Tue, Sep 22, 2015 at 5:29 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> 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
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>
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