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

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, Herv? Pag?s <hpages at fredhutch.org 
<mailto: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 <http://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


    -- 
    Herv? Pag?s

    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 <mailto:hpages at fredhutch.org>
    Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
    Fax: (206) 667-1319 <tel:%28206%29%20667-1319>