[Bioc-devel] exonsBy dropping genes from TxDb

[Hervé Pagès]

Hi Leonard,

Sorry for missing your earlier posts about this. Will look into it.

Thanks,
H.

On 10/27/2017 09:07 AM, Leonard Goldstein wrote:
> Dear bioc-devel,
>
> I noticed exonsBy is dropping a lot of genes when run on a TxDb object
> created with makeTxDbFromBiomart (see below). Please also see related post
> on the Bioconductor support site:
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_101951_-23102160&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ExVvVr6r4wUKgBmPNOQiJXSI2O1FYqFRz_llKQY_jD0&s=xUz41e2CIjMTXmO5LqkFp12ySvH9zzA0s5OMWzgWosU&e=
>
> Thanks for your help.
>
> Leonard
>
> --
>> tx <- makeTxDbFromBiomart()
>> txs_by_gene <- transcriptsBy(tx, "gene")
>> exs_by_gene <- exonsBy(tx, "gene")
>> length(txs_by_gene)
> [1] 63967
>> length(exs_by_gene)
> [1] 36751
>> subsetByOverlaps(txs_by_gene, GRanges("8", IRanges(127735434,127741434)))
> GRangesList object of length 1:
> $ENSG00000136997
> GRanges object with 9 ranges and 2 metadata columns:
>        seqnames                 ranges strand |     tx_id         tx_name
>           <Rle>              <IRanges>  <Rle> | <integer>     <character>
>    [1]        8 [127735434, 127740477]      + |    101876 ENST00000259523
>    [2]        8 [127735473, 127735817]      + |    101877 ENST00000641252
>    [3]        8 [127735519, 127738772]      + |    101878 ENST00000517291
>    [4]        8 [127736046, 127736612]      + |    101879 ENST00000641036
>    [5]        8 [127736069, 127741434]      + |    101880 ENST00000621592
>    [6]        8 [127736084, 127741434]      + |    101881 ENST00000377970
>    [7]        8 [127736220, 127741372]      + |    101882 ENST00000524013
>    [8]        8 [127736231, 127738475]      + |    101883 ENST00000520751
>    [9]        8 [127736594, 127740958]      + |    101884 ENST00000613283
>
> -------
> seqinfo: 555 sequences (1 circular) from an unspecified genome
>> subsetByOverlaps(exs_by_gene, GRanges("8", IRanges(127735434,127741434)))
> GRangesList object of length 0:
> <0 elements>
>
> -------
> seqinfo: 555 sequences (1 circular) from an unspecified genome
>> sessionInfo()
> R version 3.4.1 (2017-06-30)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: OS X El Capitan 10.11.6
>
> Matrix products: default
> BLAS:
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
> LAPACK:
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
>
> 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] stats4    parallel  stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2   Biobase_2.36.2
> [4] GenomicRanges_1.28.6   GenomeInfoDb_1.12.3    IRanges_2.10.5
> [7] S4Vectors_0.14.7       BiocGenerics_0.22.1
>
> loaded via a namespace (and not attached):
>   [1] Rcpp_0.12.13               XVector_0.16.0
>   [3] GenomicAlignments_1.12.2   zlibbioc_1.22.0
>   [5] BiocParallel_1.10.1        bit_1.1-12
>   [7] lattice_0.20-35            rlang_0.1.2
>   [9] blob_1.1.0                 tools_3.4.1
> [11] grid_3.4.1                 SummarizedExperiment_1.6.5
> [13] DBI_0.7                    matrixStats_0.52.2
> [15] bit64_0.9-7                digest_0.6.12
> [17] tibble_1.3.4               Matrix_1.2-11
> [19] GenomeInfoDbData_0.99.0    rtracklayer_1.36.6
> [21] bitops_1.0-6               RCurl_1.95-4.8
> [23] biomaRt_2.32.1             memoise_1.1.0
> [25] RSQLite_2.0                DelayedArray_0.2.7
> [27] compiler_3.4.1             Rsamtools_1.28.0
> [29] Biostrings_2.44.2          XML_3.98-1.9
> [31] pkgconfig_2.0.1
>>
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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