Extract gene annotation from Ensembl via AnnotationHub EnsDb

Retrieves gene information for a given organism from the most appropriate Ensembl database hosted via Bioconductor's AnnotationHub and ensembldb.

Usage

get_ensdb_genes(
  organism_keyword = "drosophila melanogaster",
  genome_build = NULL,
  ensembl_version = NULL,
  exclude_biotypes = c("transposable_element", "pseudogene"),
  include_gene_metadata = c("gene_id", "gene_name")
)

Arguments

organism_keyword: Character. Unique non-case-senstive string to search for the organism (e.g., "drosophila melanogaster").
genome_build: Optional character. Genome build identifier to further restrict the EnsDb selection (e.g., "BDGP6").
ensembl_version: Optional integer. Specific Ensembl version to fetch. If NULL, the latest available version is used.
exclude_biotypes: Character vector. Gene biotypes to exclude from the result (default: c("transposable_element", "pseudogene")).
include_gene_metadata: Character vector. Metadata columns to keep for each gene (default: c("gene_id", "gene_name")).

Value

List with:

genes: A GRanges object of genes (metadata columns per argument).
ensembl_version: Character. The Ensembl version string.
genome_build: Character. Genome build identifier.
species: Character. Latin binomial species name.
common_name: Character. Species common name.

Details

This function queries AnnotationHub for EnsDb objects matching a supplied organism keyword, with optional filtering by genome build and Ensembl version. Genes matching excluded biotypes are filtered out. Only user-selected metadata fields are retained in the genes output.

Examples

# \donttest{
# This example requires an internet connection and will download data.
# It is wrapped in \donttest{} so it is not run by automated checks.
dm_genes <- get_ensdb_genes(
    organism_keyword = "drosophila melanogaster",
    ensembl_version = 110
)
#> Finding genome versions ...
#> snapshotDate(): 2024-04-30
#> Loading Ensembl genome version 'Ensembl 110 EnsDb for Drosophila melanogaster'
#> loading from cache

# View the fetched genes GRanges object
dm_genes$genes
#> GRanges object with 18040 ranges and 2 metadata columns:
#>                             seqnames      ranges strand |            gene_id
#>                                <Rle>   <IRanges>  <Rle> |        <character>
#>          FBgn0259849 211000022278436   1551-2815      - |        FBgn0259849
#>          FBgn0085506 211000022278760     562-879      - |        FBgn0085506
#>          FBgn0259870 211000022279165     14-1118      - |        FBgn0259870
#>          FBgn0259817 211000022279188   1449-2180      + |        FBgn0259817
#>          FBgn0085511 211000022279264     180-614      - |        FBgn0085511
#>                  ...             ...         ...    ... .                ...
#>   FBtr0472933_df_nrg            rDNA 70297-70318      + | FBtr0472933_df_nrg
#>   FBtr0472934_df_nrg            rDNA 70330-70351      + | FBtr0472934_df_nrg
#>          FBgn0267502            rDNA 70389-70511      + |        FBgn0267502
#>          FBgn0267503            rDNA 70540-70569      + |        FBgn0267503
#>          FBgn0267504            rDNA 70955-74924      + |        FBgn0267504
#>                             gene_name
#>                           <character>
#>          FBgn0259849  Su(Ste):CR42418
#>          FBgn0085506          CG40635
#>          FBgn0259870  Su(Ste):CR42439
#>          FBgn0259817    SteXh:CG42398
#>          FBgn0085511   lncRNA:CR40719
#>                  ...              ...
#>   FBtr0472933_df_nrg                 
#>   FBtr0472934_df_nrg                 
#>          FBgn0267502 5.8SrRNA:CR45842
#>          FBgn0267503   2SrRNA:CR45843
#>          FBgn0267504  28SrRNA:CR45844
#>   -------
#>   seqinfo: 29 sequences (1 circular) from BDGP6.46 genome
# }