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List Available Annotation Tables

Source: R/annotables-data.R
ls_annotables.Rd

Lists all annotation tables that can be loaded via load_data() from the Zenodo repository (fixed Ensembl version). For the latest Ensembl annotations, use build_annotables() to query BioMart directly.

Usage

ls_annotables()

Value

a character vector of available table names.

Details

These tables have basic annotation information from Ensembl Genes for:

  • Human build 38 (grch38)

  • Human build 37 (grch37)

  • Mouse (grcm38)

  • Rat (rnor6)

  • Chicken (galgal5)

  • Worm (wbcel235)

  • Fly (bdgp6)

  • Macaque (mmul801) Where each table contains:

  • ensgene: Ensembl gene ID

  • entrez: Entrez gene ID

  • symbol: Gene symbol

  • chr: Chromosome

  • start: Start

  • end: End

  • strand: Strand

  • biotype: Protein coding, pseudogene, mitochondrial tRNA, etc.

  • description: Full gene name/description Additionally, there are tx2gene tables that link Ensembl gene IDs to Ensembl transcript IDs.

Use build_annotables() to fetch the latest annotations from Ensembl BioMart, which also supports additional organisms (dog, zebrafish, pig).

References

https://github.com/stephenturner/annotables

See also

build_annotables() for live Ensembl BioMart queries.

Examples

# \donttest{
ls_annotables()
#> Downloading https://zenodo.org/records/10360995/files/ensembl_version.rda to /tmp/Rtmpu9e9wx/ensembl_version.rda
#> Version: Ensembl Genes 105
#>  [1] "bdgp6"            "bdgp6_tx2gene"    "galgal5"          "galgal5_tx2gene" 
#>  [5] "grch37"           "grch37_tx2gene"   "grch38"           "grch38_tx2gene"  
#>  [9] "grcm38"           "grcm38_tx2gene"   "mmul801"          "mmul801_tx2gene" 
#> [13] "rnor6"            "rnor6_tx2gene"    "wbcel235"         "wbcel235_tx2gene"
load_data(ls_annotables()[1])
#> Version: Ensembl Genes 105
#> # A tibble: 28,759 × 9
#>    ensgene      entrez symbol     chr    start    end strand biotype description
#>    <chr>         <int> <chr>      <chr>  <int>  <int>  <int> <chr>   <chr>      
#>  1 FBgn0000003 3771948 7SLRNA:CR… 3R    6.82e6 6.82e6      1 ncRNA   Signal rec…
#>  2 FBgn0000008   43852 a          2R    2.21e7 2.22e7      1 protei… arc        
#>  3 FBgn0000014   42037 abd-A      3R    1.68e7 1.68e7     -1 protei… abdominal A
#>  4 FBgn0000015   47763 Abd-B      3R    1.69e7 1.70e7     -1 protei… Abdominal B
#>  5 FBgn0000017   45821 Abl        3L    1.66e7 1.66e7     -1 protei… Abl tyrosi…
#>  6 FBgn0000018   44793 abo        2L    1.10e7 1.10e7     -1 protei… abnormal o…
#>  7 FBgn0000018   76375 abo        2L    1.10e7 1.10e7     -1 protei… abnormal o…
#>  8 FBgn0000022   30981 ac         X     3.70e5 3.71e5      1 protei… achaete    
#>  9 FBgn0000024   41625 Ace        3R    1.32e7 1.33e7     -1 protei… Acetylchol…
#> 10 FBgn0000024   12038 Ace        3R    1.32e7 1.33e7     -1 protei… Acetylchol…
#> # ℹ 28,749 more rows
# }